Last Update: June 2, 2016
Table of Contents
Planned Submission Questions & Uploads
Target 1. Tobacco Mosaic Virus
Target 3. Escherichia coli GroEL
Target 7. Recombinant γ-Secretase
Overview
Welcome to the 2015/2016 EMDataBank Model Challenge! Please see the Main Model Challenge Website for overview information including goals, participation info, timeline, and target table. Refer to this guide for the challenge rules and additional target information.
Updates to this guide are being made as required; look for red text with update date.
April 28: corrected symmetry center info and BIOMT matrices for the proteasome and β-galactosidase targets.
May 3: corrected BIOMT matrices for Brome Mosaic Virus.
Questions/Comments/Suggestions? Please email challenges@emdatabank.org
Challenge Rules
- Challengers must use one or more of the map files included in the target EMDB entries as their starting point(s) for modelling. Use of the original, unmodified map from the reconstruction software, and/or independent maps generated for Fourier Shell Correlation calculation is STRONGLY encouraged (see individual target sections for filenames).
- Starting maps may be modified, e.g., filtered, sharpened, and/or segmented. If a map is modified for fitting, you will be asked to upload it along with the final model.
- The committee strongly recommends that models be validated before they are submitted, using tools of the challenger’s choosing. Tools can include, but are not limited to, those listed in the section below.
- Challengers are encouraged to explore ab initio modelling approaches, but are also permitted to utilize publicly available coordinates as starting points for fitting.
- Researchers are expected to disclose all of the prior information used in their modelling method.
- Uploaded models must:
- be positioned within the target map
- have the same symmetry as the map
- use the UNIPROT or PDB sequence/residue numbering indicated below
Validation Tools
Challengers are encouraged to validate their final model using procedures of their choosing, checking (i) internal model consistency and (ii) fit of map to the model. The software packages listed here are suggestions and are meant to serve as a starting point. Suggestions for additions to this list are welcome (challenges@emdatabank.org).
Software packages with model geometry and/or map-model fit assessment tools | Model Quality Estimation (QE) tools developed for CASP |
Planned Submission Questions & Uploads
The following information will be collected for each model challenge submission.
- Name, institution address, email, list of collaborators
- Challenge target (select from list)
- Submission Title
- Target map(s) used for fitting (checklist)
- Modelling category (choices are: 1. optimize current cryoEM model, 2. fit known related cryoEM, crystallographic, or comparative models, 3. ab initio model building, 4. any other method of map interpretation)
- Description of the modelling process
- Map preparation: description of any modifications (combination of yes/no questions and free text description)
- filtering/sharpening
- segmentation
- Source coordinates(s) used for fitting (PDB ids, free-text description of any modifications to model before use)
- Process/effort type (select from list): manual, automated, manual+automated
- Space of refinement/model optimization (select from list): real, reciprocal
- Modelling software package(s) used, with text description of parameters and settings
- Text description of the modelling process
- Was map scale adjusted as part of model optimization? (yes/no; if yes, final A/pixel).
- Estimated time/effort to create the model (cpu hours, person/days)
- Target map(s) used for validation (checklist).
- Description of validation(s) performed.
- Internal Model Consistency
- Fit of Model to the Map
- Upload: Final model file from refinement program
- Upload: Final Model in PDBx/mmCIF format, produced using PDBextract
- Upload: Map used for fitting (if modified from original)
Target 1. Tobacco Mosaic Virus
TMV Capsid Sequence: Uniprot P69687
>sp|P69687|CAPSD_TMV Capsid protein OS=Tobacco mosaic virus (strain vulgare) GN=CP PE=1 SV=2
MSYSITTPSQFVFLSSAWADPIELINLCTNALGNQFQTQQARTVVQRQFSEVWKPSPQVT
VRFPDSDFKVYRYNAVLDPLVTALLGAFDTRNRIIEVENQANPTTAETLDATRRVDDATV
AIRSAINNLIVELIRGTGSYNRSSFESSSGLVWTSGPAT
Map A:
EMDB entry: EMD-2842 primary map: emd_2842.map
Helical symmetry: rise 1.41, angle 22.03
original, unmodified map from reconstruction software: EMD-2842-full.map
maps and mask for FSC calculation: EMD-2842-half-1.map, EMD-2842-half-2.map, EMD-2842-FSC-mask.map
Target 2. T20S Proteasome
Sequences:
Proteasome Subunit alpha: Uniprot P25156
Proteasome Subunit beta: Uniprot P28061
>sp|P25156|PSA_THEAC Proteasome subunit alpha OS=Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) GN=psmA PE=1 SV=2
MQQGQMAYDRAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIE
QNSIEKIQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQM
QQYTQYGGVRPYGVSLIFAGIDQIGPRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREY
KENLPEKEAVTLGIKALKSSLEEGEELKAPEIASITVGNKYRIYDQEEVKKFL
>sp|P28061|PSB_THEAC Proteasome subunit beta OS=Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) GN=psmB PE=1 SV=1
MNQTLETGTTTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDA
QVLVRYMKAELELYRLQRRVNMPIEAVATLLSNMLNQVKYMPYMVQLLVGGIDTAPHVFS
IDAAGGSVEDIYASTGSGSPFVYGVLESQYSEKMTVDEGVDLVIRAISAAKQRDSASGGM
IDVAVITRKDGYVQLPTDQIESRIRKLGLIL
Map A:
EMDB entry: EMD-5623
D7 symmetry center position is at 128,128,128 voxels; 156.16,156.16,156.16 Å
Correction 4/28: true voxel edge is 1.2156 Å (value shown in box above is rounded)
D7 symmetry center position at 128, 128, 128 voxels; 155.5968, 155.5968, 155.5968 Å
Symmetry Matrices <==updated
primary map: emd_5623.map
original, unmodified map from reconstruction software: EMD-5623-full.map
maps for FSC calculation: EMD-5623-half-1.map, EMD-5623-half-2.map
Map B:
EMDB entry: EMD-6287
D7 symmetry center position is at 150,150,150 voxels; 147.0,147.0,147.0 Å
Correction 4/28: true voxel edge is 0.982 Å (value shown in box above is rounded)
D7 symmetry center position at 150, 150, 150 voxels: 147.3, 147.3, 147.3 Å
Symmetry Matrices <==updated
primary map: emd_6287.map
original, unmodified map from reconstruction software: EMD-6287-full.map
maps for FSC calculation: EMD-6287-half-1.map, EMD-6287-half-2.map
Target 3. Escherichia coli GroEL
GroEL Sequence: Uniprot POA6F5
>sp|P0A6F5|CH60_ECOLI 60 kDa chaperonin OS=Escherichia coli (strain K12) GN=groL PE=1 SV=2
MAAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREI
ELEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGI
DKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDG
TGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAV
AKAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTV
ISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDY
DREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALI
RVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNA
ATEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLPKNDAADLGAAGGMGG
MGGMGGMM
Map A:
EMDB entry: EMD-6422
D7 symmetry center position is at 120, 120, 120 voxels; 128.4, 128.4, 128.4 Å
(symmetry center is ok -- rechecked 4/28)
primary map: emd_6422.map
original, unmodified map from reconstruction software: EMD-6422-full.map
maps for FSC calculation: EMD-6422-half-1.map, EMD-6422-half-2.map
Target 4. TrpV1 Channel
TrpV1 Sequence: Uniprot O35433
>sp|O35433|TRPV1_RAT Transient receptor potential cation channel subfamily V member 1 OS=Rattus norvegicus GN=Trpv1 PE=1 SV=1
MEQRASLDSEESESPPQENSCLDPPDRDPNCKPPPVKPHIFTTRSRTRLFGKGDSEEASP
LDCPYEEGGLASCPIITVSSVLTIQRPGDGPASVRPSSQDSVSAGEKPPRLYDRRSIFDA
VAQSNCQELESLLPFLQRSKKRLTDSEFKDPETGKTCLLKAMLNLHNGQNDTIALLLDVA
RKTDSLKQFVNASYTDSYYKGQTALHIAIERRNMTLVTLLVENGADVQAAANGDFFKKTK
GRPGFYFGELPLSLAACTNQLAIVKFLLQNSWQPADISARDSVGNTVLHALVEVADNTVD
NTKFVTSMYNEILILGAKLHPTLKLEEITNRKGLTPLALAASSGKIGVLAYILQREIHEP
ECRHLSRKFTEWAYGPVHSSLYDLSCIDTCEKNSVLEVIAYSSSETPNRHDMLLVEPLNR
LLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEIL
SVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVAS
MVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIE
DGKNNSLPMESTPHKCRGSACKPGNSYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFI
ILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRKAF
RSGKLLQVGFTPDGKDDYRWCFRVDEVNWTTWNTNVGIINEDPGNCEGVKRTLSFSLRSG
RVSGRNWKNFALVPLLRDASTRDRHATQQEEVQLKHYTGSLKPEDAEVFKDSMVPGEK
[note added Nov 11: quote from the primary citation: "The rat TRPV1 construct used for this study consists of residues 110 to 764 (indicated by red arrows), excluding the highly divergent region (604–626, highlighted by cyan box)"]
Map A:
EMDB entry EMD-5778
Note: true voxel edge is 1.2156 Å (value shown in box above is rounded)
C4 symmetry center position is at 128, 128, (125) voxels; 0, 0, (0) Å
(symmetry center is ok -- rechecked 4/28)
primary map: emd_5778.map
original, unmodified map from reconstruction software: EMD-5778-full.map
maps for FSC calculation: EMD-5778-half-1.map, EMD-5778-half-2.map
additional maps available for this entry:
EMD-5778-full-sharpened.map
TRPV1_sharpened_-100_3.4A.map
Target 5. Brome Mosaic Virus
Symmetry: I (T=3)
BMV Capsid Sequence: Uniprot P03602
>sp|P03602|CAPSD_BMV Capsid protein OS=Brome mosaic virus GN=ORF3b PE=1 SV=1
MSTSGTGKMTRAQRRAAARRNRWTARVQPVIVEPLAAGQGKAIKAIAGYSISKWEASSDA
ITAKATNAMSITLPHELSSEKNKELKVGRVLLWLGLLPSVAGRIKACVAEKQAQAEAAFQ
VALAVADSSKEVVAAMYTDAFRGATLGDLLNLQIYLYASEAVPAKAVVVHLEVEHVRPTF
DDFFTPVYR
EMDB entry: EMD-6000
Icosahedral symmetry center position is at 210, 210, 210 voxels; 207.9, 207.9, 207.9 Å
Icosahedral orientation is n25r with 2-fold symmetry axis along y, 5-fold symmetry axis along z.
(symmetry is center ok -- rechecked 4/28)
Symmetry Matrices <==updated May 3
primary map: emd_6000.map
original, unmodified map from reconstruction software: emd_6000.map
maps for FSC calculation: BMV-set1.map, BMV-set2.map
additional segmented maps are available for this entry:
subunitA.map, subunitB.map, subunitC.map
Target 6. β-Galactosidase
Beta-galactosidase sequence: Uniprot P00722
>sp|P00722|BGAL_ECOLI Beta-galactosidase OS=Escherichia coli (strain K12) GN=lacZ PE=1 SV=2
MTMITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWR
FAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPITVNPPFVPTENP
TGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGRWVGYGQDSRLPSEFDLSAFLRA
GENRLAVMVLRWSDGSYLEDQDMWRMSGIFRDVSLLHKPTTQISDFHVATRFNDDFSRAV
LEAEVQMCGELRDYLRVTVSLWQGETQVASGTAPFGGEIIDERGGYADRVTLRLNVENPK
LWSAEIPNLYRAVVELHTADGTLIEAEACDVGFREVRIENGLLLLNGKPLLIRGVNRHEH
HPLHGQVMDEQTMVQDILLMKQNNFNAVRCSHYPNHPLWYTLCDRYGLYVVDEANIETHG
MVPMNRLTDDPRWLPAMSERVTRMVQRDRNHPSVIIWSLGNESGHGANHDALYRWIKSVD
PSRPVQYEGGGADTTATDIICPMYARVDEDQPFPAVPKWSIKKWLSLPGETRPLILCEYA
HAMGNSLGGFAKYWQAFRQYPRLQGGFVWDWVDQSLIKYDENGNPWSAYGGDFGDTPNDR
QFCMNGLVFADRTPHPALTEAKHQQQFFQFRLSGQTIEVTSEYLFRHSDNELLHWMVALD
GKPLASGEVPLDVAPQGKQLIELPELPQPESAGQLWLTVRVVQPNATAWSEAGHISAWQQ
WRLAENLSVTLPAASHAIPHLTTSEMDFCIELGNKRWQFNRQSGFLSQMWIGDKKQLLTP
LRDQFTRAPLDNDIGVSEATRIDPNAWVERWKAAGHYQAEAALLQCTADTLADAVLITTA
HAWQHQGKTLFISRKTYRIDGSGQMAITVDVEVASDTPHPARIGLNCQLAQVAERVNWLG
LGPQENYPDRLTAACFDRWDLPLSDMYTPYVFPSENGLRCGTRELNYGPHQWRGDFQFNI
SRYSQQQLMETSHRHLLHAEEGTWLNIDGFHMGIGGDDSWSPSVSAEFQLSAGRYHYQLV
WCQK
Map A:
EMDB entry EMD-5995
D2 symmetry center position at 170,170,170 voxels; 108.8, 108.8, 108.8 Å
Correction 4/28: true voxel edge is 0.6375 Å (value shown in box above is rounded)
D2 symmetry center position at 170,170,170 voxels; 108.375, 108.375, 108.375 Å
Symmetry Matrices <==updated
primary map: emd_5995.map
original, unmodified map from reconstruction software: EMD-5995-full.map
maps for FSC calculation: EMD-5995-half-1.map, EMD-5995-half-2.map
Map B:
EMDB entry EMD-2984
D2 symmetry center position at 146,146,146 voxels; 93.44, 93.44, 93.44 Å
Correction 4/27: true voxel edge is 0.637 Å (value shown in box above is rounded)
D2 symmetry center position at 146,146,146 voxels; 93.002, 93.002, 93.002 Å
Symmetry Matrices <==updated
primary map: emd_2984.map
original, unmodified map from reconstruction software: EMD-2984-full.map
maps for FSC calculation: EMD-2984-half-1.map, EMD-2984-half-2.map
Target 7. Recombinant γ-Secretase
Sequences:
Presenilin (PS1, 1-467) Uniprot P49768
PEN-2 (1-101) Uniprot Q9NZ42
APH-1 (APH-1aL, 1-265) Uniprot Q96BI3
Nicastrin (1-709) Uniprot Q92542
[note added Nov 12: For each of these sequences, the original study authors always used the 1st isoform.]
>sp|P49768|PSN1_HUMAN Presenilin-1 OS=Homo sapiens GN=PSEN1 PE=1 SV=1
MTELPAPLSYFQNAQMSEDNHLSNTVRSQNDNRERQEHNDRRSLGHPEPLSNGRPQGNSR
QVVEQDEEEDEELTLKYGAKHVIMLFVPVTLCMVVVVATIKSVSFYTRKDGQLIYTPFTE
DTETVGQRALHSILNAAIMISVIVVMTILLVVLYKYRCYKVIHAWLIISSLLLLFFFSFI
YLGEVFKTYNVAVDYITVALLIWNFGVVGMISIHWKGPLRLQQAYLIMISALMALVFIKY
LPEWTAWLILAVISVYDLVAVLCPKGPLRMLVETAQERNETLFPALIYSSTMVWLVNMAE
GDPEAQRRVSKNSKYNAESTERESQDTVAENDDGGFSEEWEAQRDSHLGPHRSTPESRAA
VQELSSSILAGEDPEERGVKLGLGDFIFYSVLVGKASATASGDWNTTIACFVAILIGLCL
TLLLLAIFKKALPALPISITFGLVFYFATDYLVQPFMDQLAFHQFYI
>sp|Q9NZ42|PEN2_HUMAN Gamma-secretase subunit PEN-2 OS=Homo sapiens GN=PSENEN PE=1 SV=1
MNLERVSNEEKLNLCRKYYLGGFAFLPFLWLVNIFWFFREAFLVPAYTEQSQIKGYVWRS
AVGFLFWVIVLTSWITIFQIYRPRWGALGDYLSFTIPLGTP
>sp|Q96BI3|APH1A_HUMAN Gamma-secretase subunit APH-1A OS=Homo sapiens GN=APH1A PE=1 SV=1
MGAAVFFGCTFVAFGPAFALFLITVAGDPLRVIILVAGAFFWLVSLLLASVVWFILVHVT
DRSDARLQYGLLIFGAAVSVLLQEVFRFAYYKLLKKADEGLASLSEDGRSPISIRQMAYV
SGLSFGIISGVFSVINILADALGPGVVGIHGDSPYYFLTSAFLTAAIILLHTFWGVVFFD
ACERRRYWALGLVVGSHLLTSGLTFLNPWYEASLLPIYAVTVSMGLWAFITAGGSLRSIQ
RSLLCRRQEDSRVMVYSALRIPPED
>sp|Q92542|NICA_HUMAN Nicastrin OS=Homo sapiens GN=NCSTN PE=1 SV=2
MATAGGGSGADPGSRGLLRLLSFCVLLAGLCRGNSVERKIYIPLNKTAPCVRLLNATHQI
GCQSSISGDTGVIHVVEKEEDLQWVLTDGPNPPYMVLLESKHFTRDLMEKLKGRTSRIAG
LAVSLTKPSPASGFSPSVQCPNDGFGVYSNSYGPEFAHCREIQWNSLGNGLAYEDFSFPI
FLLEDENETKVIKQCYQDHNLSQNGSAPTFPLCAMQLFSHMHAVISTATCMRRSSIQSTF
SINPEIVCDPLSDYNVWSMLKPINTTGTLKPDDRVVVAATRLDSRSFFWNVAPGAESAVA
SFVTQLAAAEALQKAPDVTTLPRNVMFVFFQGETFDYIGSSRMVYDMEKGKFPVQLENVD
SFVELGQVALRTSLELWMHTDPVSQKNESVRNQVEDLLATLEKSGAGVPAVILRRPNQSQ
PLPPSSLQRFLRARNISGVVLADHSGAFHNKYYQSIYDTAENINVSYPEWLSPEEDLNFV
TDTAKALADVATVLGRALYELAGGTNFSDTVQADPQTVTRLLYGFLIKANNSWFQSILRQ
DLRSYLGDGPLQHYIAVSSPTNTTYVVQYALANLTGTVVNLTREQCQDPSKVPSENKDLY
EYSWVQGPLHSNETDRLPRCVRSTARLARALSPAFELSQWSSTEYSTWTESRWKDIRARI
FLIASKELELITLTVGFGILIFSLIVTYCINAKADVLFIAPREPGAVSY
Map A:
EMDB entry: EMD-2677
primary map: emd_2677.map
original, unmodified map from reconstruction software: EMD-2677-full.map
maps for FSC calculation: EMD-2677-half-1.map, EMD-2677-half-2.map
Map B:
EMDB entry: EMD-3061
primary map: emd_3061.map
original, unmodified map from reconstruction software: EMD-3061-full.map
maps for FSC calculation: EMD-3061-half-1.map, EMD-3061-half-2.map
Target 8. 70S Ribosome
Map A (70S with EF-Tu-GDP, kirromycin, tRNAs):
EMDB entry: EMD-2847
Sequence reference: PDB entry 5afi at RCSB-PDB, PDBe, PDBj
primary map: emd_2847.map
original, unmodified map from reconstruction software: EMD-2847-full.map
maps and mask for FSC calculation: EMD-2847-half-1.map, EMD-2847-half-2.map, EMD-2847-FSC-mask.map
Map B (70S with Elongation factor G):
EMDB entry: EMD-6316
Sequence reference: PDB entry 3ja1 at RCSB-PDB, PDBe, PDBj
primary map: emd_6316.map
original, unmodified map from reconstruction software: EMD-6316-full.map
maps and mask for FSC calculation: EMD-6316-half-1.map, EMD-6316-half-2.map, EMD-6316-FSC-mask.map