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- PDB-7t15: Hexameric SIVcpz CA -

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Basic information

Entry
Database: PDB / ID: 7t15
TitleHexameric SIVcpz CA
ComponentsCapsid protein p24
KeywordsVIRAL PROTEIN / Capsid
Function / homology
Function and homology information


viral budding via host ESCRT complex / 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 p6 / Gag protein p6 / 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 nucleocapsid Gag protein p24, N-terminal / Gag protein p6 / Gag protein p6 / 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 - cpz
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsJacques, D.A. / Dickson, C.F. / 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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


Theoretical massNumber of molelcules
Total (without water)50,6442
Polymers50,6442
Non-polymers00
Water2,072115
1
A: Capsid protein p24
B: Capsid protein p24

A: Capsid protein p24
B: Capsid protein p24

A: Capsid protein p24
B: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)151,9326
Polymers151,9326
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area14920 Å2
ΔGint-75 kcal/mol
Surface area58770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.669, 90.669, 116.785
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 0 / Auth seq-ID: 1 - 219 / Label seq-ID: 1 - 219

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Capsid protein p24 /


Mass: 25321.977 Da / Num. of mol.: 2 / Mutation: P14C, E45C, W184A, M185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian immunodeficiency virus - cpz / Variant: MT145 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: Q1A241
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Crystallant: 4.5% PEG 550MME, 0.15M KSCN, 0.1M Tris (pH 9.0), 4% 2,5-hexanediol. 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: 0.91731 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91731 Å / Relative weight: 1
ReflectionResolution: 2.05→78.52 Å / Num. obs: 34170 / % possible obs: 100 % / Redundancy: 9.4 % / CC1/2: 0.987 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.027 / Rrim(I) all: 0.084 / Net I/σ(I): 12.8 / Num. measured all: 321339 / Scaling rejects: 125
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.05-2.119.50.9632513926580.8470.331.0182.3
8.94-78.529.20.03440244390.9730.0140.03837

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.96 Å65.16 Å
Translation3.96 Å65.16 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.5.8data scaling
PHASER2.5.7phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H47

3h47


Resolution: 2.05→65.25 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 9.672 / SU ML: 0.125 / SU R Cruickshank DPI: 0.1814 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 1612 4.7 %RANDOM
Rwork0.2018 ---
obs0.2032 32525 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.71 Å2 / Biso mean: 45.885 Å2 / Biso min: 25.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å2-0.4 Å2-0 Å2
2---0.79 Å20 Å2
3---2.57 Å2
Refinement stepCycle: final / Resolution: 2.05→65.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3275 0 0 115 3390
Biso mean---44.69 -
Num. residues----425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133436
X-RAY DIFFRACTIONr_bond_other_d0.0090.0153315
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.654692
X-RAY DIFFRACTIONr_angle_other_deg1.3471.5767645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.775449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.14722.759174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69415596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.0011524
X-RAY DIFFRACTIONr_chiral_restr0.0710.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024443
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02757
Refine LS restraints NCS

Ens-ID: 1 / Number: 6783 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 96 -
Rwork0.305 2431 -
all-2527 -
obs--99.96 %
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)
13.2071.69861.81562.40541.53842.52620.1374-0.1829-0.07250.3291-0.15830.18060.1531-0.16490.02090.058-0.00520.05130.03250.02120.0684-70.9808-17.6302-6.1412
21.2057-0.4449-0.33714.53652.02061.8161-0.1006-0.173-0.11370.36920.0660.12650.1573-0.03530.03460.04540.0062-0.00220.04830.04280.0514-65.3586-44.4056-6.5285
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 220
2X-RAY DIFFRACTION2B1 - 219

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