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- PDB-7t14: Hexameric SIVmac CA -

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Basic information

Entry
Database: PDB / ID: 7t14
TitleHexameric SIVmac CA
ComponentsCapsid protein p24
KeywordsVIRAL PROTEIN / Capsid
Function / homology
Function and homology information


viral process / viral nucleocapsid / host cell cytoplasm / host cell nucleus / structural molecule activity / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Retroviral nucleocapsid Gag protein p24, N-terminal / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal ...Retroviral nucleocapsid Gag protein p24, N-terminal / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesSimian immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsJacques, D.A. / James, L.C.
Funding support Australia, United Kingdom, European Union, 6items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP180101384 Australia
National Health and Medical Research Council (NHMRC, Australia)GNT1158338 Australia
Wellcome Trust214344/Z/18/Z United Kingdom
Wellcome Trust108183 United Kingdom
Wellcome Trust220863 United Kingdom
European Research Council (ERC)339223European Union
CitationJournal: Nat Microbiol / Year: 2022
Title: Evasion of cGAS and TRIM5 defines pandemic HIV.
Authors: Zuliani-Alvarez, L. / Govasli, M.L. / Rasaiyaah, J. / Monit, C. / Perry, S.O. / Sumner, R.P. / McAlpine-Scott, S. / Dickson, C. / Rifat Faysal, K.M. / Hilditch, L. / Miles, R.J. / Bibollet- ...Authors: Zuliani-Alvarez, L. / Govasli, M.L. / Rasaiyaah, J. / Monit, C. / Perry, S.O. / Sumner, R.P. / McAlpine-Scott, S. / Dickson, C. / Rifat Faysal, K.M. / Hilditch, L. / Miles, R.J. / Bibollet-Ruche, F. / Hahn, B.H. / Boecking, T. / Pinotsis, N. / James, L.C. / Jacques, D.A. / Towers, G.J.
History
DepositionDec 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Capsid protein p24
B: Capsid protein p24
C: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)76,4583
Polymers76,4583
Non-polymers00
Water9,242513
1
A: Capsid protein p24
x 6


Theoretical massNumber of molelcules
Total (without water)152,9166
Polymers152,9166
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
crystal symmetry operation4_755-x+2,-y,z1
crystal symmetry operation5_665y+1,-x+y+1,z1
crystal symmetry operation6_545x-y,x-1,z1
Buried area11720 Å2
ΔGint-67 kcal/mol
Surface area62580 Å2
MethodPISA
2
B: Capsid protein p24
C: Capsid protein p24

B: Capsid protein p24
C: Capsid protein p24

B: Capsid protein p24
C: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)152,9166
Polymers152,9166
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area11880 Å2
ΔGint-74 kcal/mol
Surface area61170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.102, 153.102, 62.540
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Capsid protein p24 /


Mass: 25486.045 Da / Num. of mol.: 3 / Mutation: P13C, E44C, W182A, M183A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian immunodeficiency virus (MM251 ISOLATE)
Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: A0A7D6GPL1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 2.77 Å3/Da / Density % sol: 55.55 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: Crystallant: 10% (w/v) PEG 6000, 5% (w/v) MPD, 100 mM HEPES (pH 7.5). Crystals grew in 200 nL protein (12 mg/ml) + 200 nL crystallant. Cryoprotected in 20% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.25→29.29 Å / Num. obs: 39855 / % possible obs: 99.4 % / Redundancy: 5.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.078 / Rrim(I) all: 0.18 / Net I/σ(I): 9.7 / Num. measured all: 206402
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
2.25-2.325.20.7241830235160.7820.3480.8052.695.6
8.99-29.295.30.03334366540.9990.0160.03734.897.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.98 Å29.29 Å
Translation4.98 Å29.29 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.3.8data scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H47

3h47


Resolution: 2.25→29.29 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.914 / SU B: 11.642 / SU ML: 0.149 / SU R Cruickshank DPI: 0.2543 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.254 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 1934 4.9 %RANDOM
Rwork0.1889 ---
obs0.1908 37920 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.75 Å2 / Biso mean: 26.719 Å2 / Biso min: 7.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å20 Å2
2--0.11 Å2-0 Å2
3----0.36 Å2
Refinement stepCycle: final / Resolution: 2.25→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4987 0 0 513 5500
Biso mean---33.77 -
Num. residues----647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195095
X-RAY DIFFRACTIONr_bond_other_d0.0010.024813
X-RAY DIFFRACTIONr_angle_refined_deg0.9061.9596940
X-RAY DIFFRACTIONr_angle_other_deg0.73311057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6055643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41725.365233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26515832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6141527
X-RAY DIFFRACTIONr_chiral_restr0.050.2774
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215886
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021135
LS refinement shellResolution: 2.25→2.307 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.277 130 -
Rwork0.231 2699 -
obs--96.22 %
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)
12.4295-0.0214-2.12141.08831.28149.77840.02340.02210.1582-0.06790.0169-0.0304-0.11060.354-0.04040.01260.00230.0090.02410.02610.1063143.618-11.2839-23.4208
20.89840.0363-0.5111.11560.19993.048-0.03540.17710.0161-0.1862-0.02240.12490.1373-0.22140.05770.054-0.0007-0.01480.0453-0.00110.0956131.5089-19.6973-25.5575
32.3395-1.1137-0.32113.18950.75581.699-0.0974-0.1417-0.07510.15450.09530.14880.0545-0.05760.00210.00890.00740.01080.02270.01790.069115.53643.4963-2.4043
41.87870.6754-1.58891.7019-3.15610.85770.0084-0.07220.06180.0695-0.00890.064-0.0544-0.27710.00050.0235-0.0050.01640.0246-0.0260.115290.6975-47.52117.7488
51.0007-0.4344-0.31841.4531-0.5892.4417-0.0835-0.1730.05050.2882-0.0639-0.1757-0.01630.21970.14740.0651-0.0059-0.04920.0568-0.00620.1551105.4674-47.29549.5015
60.98910.55130.06394.5063-0.6591.1309-0.0929-0.0291-0.0575-0.3668-0.0083-0.26530.01630.00760.10110.0445-0.02050.02120.0452-0.0040.1165105.0802-19.614-13.3562
71.6174-0.52952.50663.1064-3.52219.62030.0352-0.0506-0.09270.086-0.06010.13350.27580.04320.02490.0350.00280.03780.0561-0.00460.139286.6574-33.52277.8922
80.87970.27570.07731.2996-0.7482.94510.0126-0.1830.07720.2871-0.055-0.0306-0.26650.14210.04250.0717-0.0148-0.01460.0756-0.0320.131393.7791-20.59229.9581
96.6184-1.91590.05091.8917-0.21982.52540.16810.31610.3993-0.0971-0.1551-0.1765-0.1669-0.0346-0.0130.03710.01380.02380.02010.03190.112768.0976-8.2724-14.7687
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 30
2X-RAY DIFFRACTION2A31 - 141
3X-RAY DIFFRACTION3A142 - 217
4X-RAY DIFFRACTION4B1 - 30
5X-RAY DIFFRACTION5B31 - 141
6X-RAY DIFFRACTION6B142 - 217
7X-RAY DIFFRACTION7C1 - 30
8X-RAY DIFFRACTION8C31 - 141
9X-RAY DIFFRACTION9C142 - 217

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