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- PDB-7s94: Structure of the core postfusion porcine endogenous retrovirus fu... -

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Basic information

Entry
Database: PDB / ID: 7s94
TitleStructure of the core postfusion porcine endogenous retrovirus fusion protein
ComponentsEndogenous retrovirus group S71 member 1 Env polyprotein
KeywordsVIRAL PROTEIN / fusion protein / glycoprotein
Function / homologyF-MuLV receptor-binding / ENV polyprotein (coat polyprotein) / TLV/ENV coat polyprotein / membrane => GO:0016020 / DI(HYDROXYETHYL)ETHER / Endogenous retrovirus group S71 member 1 Env polyprotein
Function and homology information
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDean, T.T. / Lee, J.E.
Funding support Canada, 3items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-173301 Canada
Canada Research Chairs Canada
Canada Foundation for Innovation Canada
CitationJournal: Mbio / Year: 2022
Title: Structure of the Core Postfusion Porcine Endogenous Retrovirus Fusion Protein.
Authors: Dean, T.T. / Serrao, V.H.B. / Lee, J.E.
History
DepositionSep 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 7, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endogenous retrovirus group S71 member 1 Env polyprotein
B: Endogenous retrovirus group S71 member 1 Env polyprotein
C: Endogenous retrovirus group S71 member 1 Env polyprotein
D: Endogenous retrovirus group S71 member 1 Env polyprotein
E: Endogenous retrovirus group S71 member 1 Env polyprotein
F: Endogenous retrovirus group S71 member 1 Env polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,28610
Polymers66,0036
Non-polymers2834
Water5,585310
1
A: Endogenous retrovirus group S71 member 1 Env polyprotein
B: Endogenous retrovirus group S71 member 1 Env polyprotein
C: Endogenous retrovirus group S71 member 1 Env polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1435
Polymers33,0013
Non-polymers1422
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9280 Å2
ΔGint-88 kcal/mol
Surface area13740 Å2
MethodPISA
2
D: Endogenous retrovirus group S71 member 1 Env polyprotein
E: Endogenous retrovirus group S71 member 1 Env polyprotein
F: Endogenous retrovirus group S71 member 1 Env polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1435
Polymers33,0013
Non-polymers1422
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-79 kcal/mol
Surface area12650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.860, 34.219, 100.445
Angle α, β, γ (deg.)90.000, 99.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Endogenous retrovirus group S71 member 1 Env polyprotein / Putative envelope polyprotein


Mass: 11000.478 Da / Num. of mol.: 6 / Mutation: C557S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Escherichia coli (E. coli) / References: UniProt: B3VQ66
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 24% (w/v) PEG 1500 and 20% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 6, 2020
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2→47.73 Å / Num. obs: 41923 / % possible obs: 93.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 19.55 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.066 / Rrim(I) all: 0.175 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.054.20.605829119700.6530.3160.6883.160.4
8.93-47.737.30.1141145660.9910.0410.11711.298.9

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JGS

4jgs


Resolution: 2→47.7 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 3933 5 %random
Rwork0.1745 74686 --
obs0.1767 41916 91.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.02 Å2 / Biso mean: 28.258 Å2 / Biso min: 8.1 Å2
Refinement stepCycle: final / Resolution: 2→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4012 0 36 310 4358
Biso mean--50.82 32.1 -
Num. residues----527
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.020.2552660.22291479154549
2.02-2.050.24861030.20761720182360
2.05-2.080.251940.20441815190963
2.08-2.10.3002930.19972097219071
2.1-2.130.20981030.20072222232575
2.13-2.170.24221040.18482271237578
2.17-2.20.23741090.18062512262186
2.2-2.240.25721420.1792889303197
2.24-2.270.20811580.1742849300798
2.27-2.320.23181230.16592913303699
2.32-2.360.24141530.16432878303199
2.36-2.410.24371260.1622923304999
2.41-2.460.21371280.1642954308299
2.46-2.520.22121340.16032856299099
2.52-2.580.22621670.17022930309799
2.58-2.650.22891780.17412878305699
2.65-2.730.22321560.17172862301899
2.73-2.820.22831340.16682950308499
2.82-2.920.2311420.16612874301699
2.92-3.030.18641520.16752893304598
3.03-3.170.19051690.17242842301199
3.17-3.340.20331740.1642883305799
3.34-3.550.19292020.1532834303699
3.55-3.820.16491780.149929283106100
3.82-4.210.19681590.15252850300999
4.21-4.810.19961800.1582849302998
4.82-6.060.23541360.22532853298998
6.07-47.70.28751700.23622882305299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5046-1.3413-2.30710.75840.77162.99560.04070.1959-0.4925-0.1089-0.1242-0.01210.1102-0.33020.00180.1946-0.0214-0.04610.1452-0.06880.24331.1163-10.517969.3953
22.0595-0.5397-0.80441.79730.8993.14170.09360.21930.19140.1026-0.16520.3784-0.2852-0.5476-0.02220.18040.04520.0480.60270.00410.358810.92541.801886.0982
35.1752-0.66230.2580.3759-0.02870.08090.12290.0636-0.4365-0.07-0.02250.13140.0343-0.0584-0.07140.1110.0034-0.0240.12320.00260.1578-10.201-3.398938.5466
41.7249-0.27380.03990.49710.10770.19320.1074-0.67760.3220.0627-0.0178-0.1262-0.11450.1396-0.05990.168-0.03680.01430.2067-0.01980.200716.97116.274344.6349
56.90411.3112-0.31942.4075-0.43992.12020.1401-0.1486-0.0694-0.00940.03590.18620.1222-0.1145-0.14030.1539-0.0032-0.02990.15070.04410.1812-17.4747-3.890946.5056
64.9069-1.47940.09380.6821-0.01740.07030.22670.24640.0487-0.2008-0.12690.0376-0.0136-0.0373-0.07720.14980.037-0.02190.15980.00310.1495-9.24132.18531.5235
71.8705-0.68920.49670.2898-0.34940.7177-0.0083-0.0634-0.2869-0.02490.0199-0.03120.26730.0576-0.04520.24650.0393-0.04320.1570.01340.23615.0224-12.187741.1948
86.5893-2.19421.5333.7152-0.73093.01210.19640.4472-0.235-0.3475-0.05590.2997-0.0592-0.4789-0.09360.18690.0454-0.03740.3174-0.05490.2063-14.7352-4.58126.1085
94.6442-0.34360.18660.31110.10530.29250.1973-0.17950.3226-0.0301-0.05490.0337-0.0654-0.084-0.10050.10840.0153-0.0070.11570.02230.1222-9.47925.52439.796
100.1971-0.1322-0.37140.66090.65571.4610.11470.1676-0.0186-0.09670.1588-0.237-0.00780.2836-0.17830.13750.02230.04010.2229-0.01570.157317.0274-0.120427.0405
115.5263-1.4748-2.98211.23080.59782.52160.2694-0.03480.37240.0292-0.15630.0517-0.2216-0.0733-0.04960.18040.01980.01320.18030.02740.2268-17.128914.040338.5381
121.19210.39720.17771.03060.27911.49870.1408-0.0594-0.00690.17830.00310.1005-0.3084-0.0641-0.1370.16840.00610.01610.08630.01180.118131.9821.107982.053
131.04640.7301-1.15291.7845-2.31734.73650.06910.0017-0.06520.37970.0438-0.0709-0.6926-0.1137-0.12620.3086-0.00060.07340.19460.03630.124523.9561-0.3128104.8441
140.38370.0550.37081.34010.55021.69550.1038-0.1839-0.390.0874-0.08150.04260.1379-0.0753-0.030.0941-0.0453-0.02270.09360.01390.122731.9433-6.307279.3612
155.49663.3087-1.50313.5289-1.09131.7817-0.07280.1325-0.2685-0.02570.0487-0.3470.13290.3204-0.00720.16550.037-0.02440.176-0.03050.164942.9628-4.514883.1909
166.41831.9325-1.94741.8162-0.83322.155-0.0348-0.0407-0.69720.1893-0.03440.23210.7099-0.62280.09480.4707-0.12370.09770.28780.01840.375321.0713-15.9591.6804
171.99380.0521-1.63210.90820.20812.97450.05420.1194-0.14880.0858-0.10690.2019-0.3371-0.5501-0.01020.12820.03370.02730.19330.0280.13323.25031.291284.4272
182.41780.4474-0.04223.0918-0.51083.33270.0451-0.0587-0.3863-0.306-0.06980.22850.1121-0.02010.03110.2548-0.04250.02030.1902-0.11630.230140.9813-7.765559.0948
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'F' and (resid 552 through 562 )F552 - 562
2X-RAY DIFFRACTION2chain 'F' and (resid 563 through 579 )F563 - 579
3X-RAY DIFFRACTION3chain 'A' and (resid 491 through 541 )A491 - 541
4X-RAY DIFFRACTION4chain 'A' and (resid 542 through 562 )A542 - 562
5X-RAY DIFFRACTION5chain 'A' and (resid 563 through 582 )A563 - 582
6X-RAY DIFFRACTION6chain 'B' and (resid 492 through 541 )B492 - 541
7X-RAY DIFFRACTION7chain 'B' and (resid 542 through 562 )B542 - 562
8X-RAY DIFFRACTION8chain 'B' and (resid 563 through 580 )B563 - 580
9X-RAY DIFFRACTION9chain 'C' and (resid 491 through 541 )C491 - 541
10X-RAY DIFFRACTION10chain 'C' and (resid 542 through 562 )C542 - 562
11X-RAY DIFFRACTION11chain 'C' and (resid 563 through 587 )C563 - 587
12X-RAY DIFFRACTION12chain 'D' and (resid 498 through 562 )D498 - 562
13X-RAY DIFFRACTION13chain 'D' and (resid 563 through 587 )D563 - 587
14X-RAY DIFFRACTION14chain 'E' and (resid 502 through 552 )E502 - 552
15X-RAY DIFFRACTION15chain 'E' and (resid 553 through 562 )E553 - 562
16X-RAY DIFFRACTION16chain 'E' and (resid 563 through 577 )E563 - 577
17X-RAY DIFFRACTION17chain 'F' and (resid 497 through 541 )F497 - 541
18X-RAY DIFFRACTION18chain 'F' and (resid 542 through 551 )F542 - 551

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