Last Update: June 2, 2016

Table of Contents

Overview

Challenge Rules

Validation Tools

Planned Submission Questions & Uploads

Target 1. Tobacco Mosaic Virus

Target 2. T20S Proteasome

Target 3. Escherichia coli GroEL

Target 4. TrpV1 Channel

Target 5. Brome Mosaic Virus

Target 6. β-Galactosidase

Target 7. Recombinant γ-Secretase

Target 8. 70S Ribosome

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

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.

  1. Name, institution address, email, list of collaborators
  2. Challenge target  (select from list)
  3. Submission Title
  4. Target map(s) used for fitting (checklist)
  5. 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)
  6. Description of the modelling process
  1. Map preparation: description of any modifications (combination of yes/no questions and free text description)
  1. filtering/sharpening
  2. segmentation
  1. Source coordinates(s) used for fitting (PDB ids, free-text description of any modifications to model before use)
  2. Process/effort type (select from list): manual, automated, manual+automated
  3. Space of refinement/model optimization (select from list): real, reciprocal
  4. Modelling software package(s) used, with text description of parameters and settings
  5. Text description of the modelling process
  6. Was map scale adjusted as part of model optimization? (yes/no; if yes, final A/pixel).
  7. Estimated time/effort to create the model (cpu hours, person/days)
  1. Target map(s) used for validation (checklist).
  2. Description of validation(s) performed.
  1. Internal Model Consistency
  2. Fit of Model to the Map
  1. Upload: Final model file from refinement program
  2. Upload: Final Model in PDBx/mmCIF format, produced using PDBextract
  3. 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

Symmetry Matrices

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)

Symmetry Matrices

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)

Symmetry Matrices

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