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- PDB-4jmr: A unique spumavirus gag N-terminal domain with functional propert... -

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Basic information

Entry
Database: PDB / ID: 4jmr
TitleA unique spumavirus gag N-terminal domain with functional properties of orthoretroviral Matrix and Capsid
Components
  • Env protein
  • Gag proteinHIV-1 protease
KeywordsViral protein/PEPTIDE / Gag / Env / coiled-coil / Viral protein / Viral protein-PEPTIDE complex
Function / homology
Function and homology information


host cytoskeleton / microtubule-dependent intracellular transport of viral material towards nucleus / viral budding via host ESCRT complex / viral release from host cell / viral capsid / viral nucleocapsid / host cell cytoplasm / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / symbiont entry into host cell ...host cytoskeleton / microtubule-dependent intracellular transport of viral material towards nucleus / viral budding via host ESCRT complex / viral release from host cell / viral capsid / viral nucleocapsid / host cell cytoplasm / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / symbiont entry into host cell / viral envelope / host cell nucleus / endoplasmic reticulum membrane / virion membrane / DNA binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
Foamy virus envelope protein / Foamy virus envelope protein / Gag polyprotein / : / : / Spumavirus gag protein, N-terminal / Spumavirus Gag polyprotein, conserved central domain / Spumavirus Gag polyprotein, C-terminal / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1500 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Foamy virus envelope protein / Foamy virus envelope protein / Gag polyprotein / : / : / Spumavirus gag protein, N-terminal / Spumavirus Gag polyprotein, conserved central domain / Spumavirus Gag polyprotein, C-terminal / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1500 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Gag polyprotein / Gag polyprotein / Env leader protein
Similarity search - Component
Biological speciesHuman foamy virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsTaylor, I.A. / Goldstone, D.C. / Flower, T.G. / Ball, N.J.
CitationJournal: Plos Pathog. / Year: 2013
Title: A Unique Spumavirus Gag N-terminal Domain with Functional Properties of Orthoretroviral Matrix and Capsid.
Authors: Goldstone, D.C. / Flower, T.G. / Ball, N.J. / Sanz-Ramos, M. / Yap, M.W. / Ogrodowicz, R.W. / Stanke, N. / Reh, J. / Lindemann, D. / Stoye, J.P. / Taylor, I.A.
History
DepositionMar 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Source and taxonomy
Category: entity_src_gen / pdbx_entity_src_syn ...entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num ..._entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num
Revision 1.2Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gag protein
B: Gag protein
C: Gag protein
D: Gag protein
F: Env protein
E: Env protein
G: Env protein
H: Env protein


Theoretical massNumber of molelcules
Total (without water)101,2998
Polymers101,2998
Non-polymers00
Water1629
1
A: Gag protein
B: Gag protein
F: Env protein
G: Env protein


Theoretical massNumber of molelcules
Total (without water)50,6504
Polymers50,6504
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-49 kcal/mol
Surface area19030 Å2
MethodPISA
2
C: Gag protein
D: Gag protein
E: Env protein
H: Env protein


Theoretical massNumber of molelcules
Total (without water)50,6504
Polymers50,6504
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-43 kcal/mol
Surface area17980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.411, 122.365, 61.766
Angle α, β, γ (deg.)90.000, 97.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Gag protein / HIV-1 protease


Mass: 22867.793 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human foamy virus / Gene: gag / Plasmid: pET47b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: A0A1Q1N9V7, UniProt: P14349*PLUS
#2: Protein/peptide
Env protein


Mass: 2457.031 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: Naturally occurring sequence of the Env leader peptide
Source: (synth.) Human foamy virus / References: UniProt: Q98830
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5
Details: 500uM 1:1 complex mixed with an equal volume 10% PEG 4000, 20% glycerol, 30mM MgCl2, 30mM CaCl2, 100mM Tris-Bicine pH 8.5, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2011
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.9→45.53 Å / Num. obs: 19334 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Biso Wilson estimate: 52.765 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 14.55
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.9-30.3224.2865491891199.6
3-3.10.2495.45548416471100
3.1-3.20.2046.6548801421199.7
3.2-3.30.1677.6942741277199.2
3.3-3.40.1419.5383111151100
3.4-3.50.10911.1134281007199.6
3.5-40.07215.13119523608199.1
4-50.04621.57117173579199.1
5-60.04421.7653091591198.8
6-80.04223.3641201265198.8
8-100.03228.851474459198.3
10-45.50.03129.371485474196.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.9 Å45.53 Å
Translation2.9 Å45.53 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
GDAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→45.53 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.886 / WRfactor Rfree: 0.2714 / WRfactor Rwork: 0.2262 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.785 / SU B: 45.196 / SU ML: 0.383 / SU R Cruickshank DPI: 2.2075 / SU Rfree: 0.4568 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.208 / ESU R Free: 0.457 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2714 993 5.1 %RANDOM
Rwork0.2262 ---
all0.2262 19468 --
obs0.2285 19331 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.55 Å2 / Biso mean: 47.8143 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.07 Å2
2--0.01 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.9→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5902 0 0 9 5911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0196051
X-RAY DIFFRACTIONr_angle_refined_deg0.8391.978245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2135728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56624.317315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.798151018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.471555
X-RAY DIFFRACTIONr_chiral_restr0.0510.2915
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0214697
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 75 -
Rwork0.324 1334 -
all-1409 -
obs--99.65 %
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)
14.81930.22990.03744.00164.53216.22820.031-0.3199-0.10780.52560.1389-0.02660.76330.8991-0.16990.23440.0999-0.03520.10730.00530.254-11.999-41.907-20.42
26.4648-2.99633.60365.7478-1.79965.65290.2077-0.2505-0.09110.4032-0.0567-0.32570.37890.5273-0.1510.2391-0.0053-0.02050.1695-0.06350.1744-11.969-33.66-14.667
31.2029-0.31550.05564.59620.1121.1116-0.13530.0586-0.06310.01140.0468-0.1660.13750.15340.08850.13740.0343-0.01840.1982-0.05510.1095-17.554-20.976-20.855
40.26410.24342.12221.1783-1.219433.1477-0.16660.10840.1459-0.5982-0.01160.1996-1.05270.60280.17820.56950.08090.06320.4454-0.01410.2738-19.787-3.856-45.852
57.8519-0.03880.16374.4563-1.518114.7222-0.0997-0.18650.27220.28120.01650.0878-0.2513-0.09810.08320.05120.0071-0.02290.0167-0.04920.1728-34.87122.51-17.868
66.4077-5.1129-1.46526.58083.45315.0832-0.0222-0.29240.19850.1662-0.01950.0337-0.2464-0.21950.04170.1781-0.094-0.00710.10920.00050.0544-35.87215.089-13.997
71.5455-1.2231-0.59994.48610.09320.6096-0.025-0.0024-0.04410.06810.05310.20180.0147-0.0284-0.02810.1152-0.0370.02840.15450.01630.0301-29.5741.757-21.222
83.47150.1141-11.36850.0171-0.351337.3325-0.34930.2693-0.1428-0.1046-0.0409-0.02140.8962-0.75070.39020.73970.12020.01580.489-0.01360.3213-22.215-12.479-49.769
95.32090.5616-2.5084.4231-3.2949.13450.2112-0.41150.60360.24270.03880.5597-0.2653-0.9037-0.250.26070.06660.00150.2558-0.04770.5511-9.06837.59-23.436
105.7753-4.2764-2.31816.19961.59363.56330.0442-0.24450.3550.42430.10040.5407-0.3881-0.2997-0.14470.2135-0.04630.01790.23790.00090.3673-9.57329.688-17.643
111.9564-0.1221-0.49284.7045-0.23660.9345-0.0961-0.10550.0004-0.1150.03780.341-0.0926-0.26750.05830.09440.0208-0.0150.22250.00170.1868-3.73416.574-22.241
120.12330.04760.22562.85676.396423.15670.03820.2553-0.1803-0.93740.240.24980.16990.2553-0.27820.9423-0.0207-0.20890.7359-0.11710.5896-0.445-2.913-45.806
135.53360.10650.33086.8928-1.584613.9558-0.2209-0.2347-0.44960.25360.15780.34240.95280.34910.06310.09860.05420.01910.10440.01420.365513.33-26.492-15.154
147.6169-4.68552.99814.9735-3.74635.1826-0.215-0.3182-0.25840.28860.02880.02290.2490.29730.18620.1813-0.00930.02720.1373-0.02350.286114.7-18.9-11.736
151.7424-0.74930.40634.8907-1.43150.7577-0.0714-0.0022-0.16960.07880.0094-0.21070.07320.04420.0620.1018-0.0183-0.04570.1763-0.02080.26028.193-6.175-19.981
164.2746-4.17612.28884.1583-12.549439.7180.7155-0.0115-0.7825-0.51470.13140.55160.2226-0.138-0.84691.3462-0.2694-0.26490.7214-0.16530.75251.7785.556-49.964
170.1061-0.85490.35837.2247-3.06881.3086-0.01880.0125-0.07670.5920.0220.2291-0.25990.0125-0.00330.2894-0.05620.03050.4421-0.10350.527124.005-31.056-10.945
1813.060211.6829-11.528410.4529-10.313810.19020.49810.7652-0.24841.05080.0449-0.2322-1.0511-0.7345-0.54290.45450.2050.12410.46990.33341.152319.774-37.399-5.899
1914.4346-14.46594.565315.4118-2.64695.54760.0153-0.4785-0.17650.20310.14290.15870.3892-0.7814-0.15820.3304-0.13870.07790.4131-0.09630.3577-50.59725.058-12.274
2014.814-5.94091.879812.7191-0.82240.2399-0.3295-0.4520.849-1.10520.2694-0.6232-0.036-0.06040.06010.24030.04190.05160.1464-0.06580.3199-41.07830.267-14.144
2127.957513.635518.46286.69118.334624.12211.7738-0.4873-0.16821.365-0.8672-0.0816-2.34330.2189-0.90661.4841-0.24370.16690.2682-0.24670.9532-40.86934.749-6.998
2237.4129-13.08559.69245.39420.028216.932-0.4158-0.0264-1.03070.1123-0.07580.4896-0.4445-0.25380.49160.64490.1439-0.32840.4634-0.04930.6548-0.641-45.361-15.759
2329.0509-24.8451-8.645446.08751.01240.27580.71540.4198-0.64020.3247-0.90260.5240.56252.58340.18720.27410.1505-0.05330.46150.04730.3937-5.709-50.823-12.483
243.2112-6.0864-3.593511.78517.22184.70350.16430.04830.8716-0.44560.0271-1.2259-0.59850.0366-0.19140.71810.0204-0.260.50.06781.1475-19.01742.144-21.486
250.3337-2.5342-0.058420.35370.52730.0179-0.5824-0.19110.31741.2280.9671-2.1947-0.03180.0252-0.38471.02740.2239-0.02420.5414-0.22910.791-15.06849.107-15.757
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 30
2X-RAY DIFFRACTION2A31 - 75
3X-RAY DIFFRACTION3A76 - 154
4X-RAY DIFFRACTION4A155 - 179
5X-RAY DIFFRACTION5B7 - 30
6X-RAY DIFFRACTION6B31 - 74
7X-RAY DIFFRACTION7B75 - 158
8X-RAY DIFFRACTION8B159 - 179
9X-RAY DIFFRACTION9C9 - 30
10X-RAY DIFFRACTION10C31 - 75
11X-RAY DIFFRACTION11C76 - 154
12X-RAY DIFFRACTION12C155 - 174
13X-RAY DIFFRACTION13D7 - 30
14X-RAY DIFFRACTION14D31 - 74
15X-RAY DIFFRACTION15D75 - 158
16X-RAY DIFFRACTION16D159 - 173
17X-RAY DIFFRACTION17E2 - 10
18X-RAY DIFFRACTION18E11 - 15
19X-RAY DIFFRACTION19F1 - 6
20X-RAY DIFFRACTION20F7 - 12
21X-RAY DIFFRACTION21F13 - 17
22X-RAY DIFFRACTION22G3 - 9
23X-RAY DIFFRACTION23G10 - 13
24X-RAY DIFFRACTION24H5 - 9
25X-RAY DIFFRACTION25H10 - 17

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