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- PDB-6obh: Structure of HIV-1 CA 1/2-hexamer -

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Basic information

Entry
Database: PDB / ID: 6obh
TitleStructure of HIV-1 CA 1/2-hexamer
Components(CA) x 3
KeywordsVIRAL PROTEIN / capsid / disulfide
Function / homology
Function and homology information


viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity ...viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain ...Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Gag polyprotein / Gag polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsSummers, B.J. / Xiong, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2P50GM082251-11 United States
CitationJournal: Cell Host Microbe / Year: 2019
Title: Modular HIV-1 Capsid Assemblies Reveal Diverse Host-Capsid Recognition Mechanisms.
Authors: Summers, B.J. / Digianantonio, K.M. / Smaga, S.S. / Huang, P.T. / Zhou, K. / Gerber, E.E. / Wang, W. / Xiong, Y.
History
DepositionMar 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CA
B: CA
C: CA
D: CA
E: CA
F: CA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,73712
Polymers153,5996
Non-polymers1386
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The assembly eluted at the proper position to indicate the correct size.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15700 Å2
ΔGint-128 kcal/mol
Surface area61410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.770, 77.746, 77.758
Angle α, β, γ (deg.)70.65, 70.70, 70.59
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNAA1 - 2192 - 220
21GLNGLNBB1 - 2192 - 220
12GLYGLYAA1 - 2202 - 221
22GLYGLYCC1 - 2202 - 221
13GLNGLNAA1 - 2192 - 220
23GLNGLNDD1 - 2192 - 220
14GLYGLYAA1 - 2202 - 221
24GLYGLYEE1 - 2202 - 221
15GLNGLNAA1 - 2192 - 220
25GLNGLNFF1 - 2192 - 220
16GLNGLNBB1 - 2192 - 220
26GLNGLNCC1 - 2192 - 220
17VALVALBB1 - 2212 - 222
27VALVALDD1 - 2212 - 222
18GLNGLNBB1 - 2192 - 220
28GLNGLNEE1 - 2192 - 220
19VALVALBB1 - 2212 - 222
29VALVALFF1 - 2212 - 222
110GLNGLNCC1 - 2192 - 220
210GLNGLNDD1 - 2192 - 220
111GLYGLYCC1 - 2202 - 221
211GLYGLYEE1 - 2202 - 221
112GLNGLNCC1 - 2192 - 220
212GLNGLNFF1 - 2192 - 220
113GLNGLNDD1 - 2192 - 220
213GLNGLNEE1 - 2192 - 220
114VALVALDD1 - 2212 - 222
214VALVALFF1 - 2212 - 222
115GLNGLNEE1 - 2192 - 220
215GLNGLNFF1 - 2192 - 220

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein CA


Mass: 25618.439 Da / Num. of mol.: 2 / Fragment: UNP residues 107-337 / Mutation: A14C, W184A, M185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T2CI25, UniProt: P12493*PLUS
#2: Protein CA


Mass: 25562.441 Da / Num. of mol.: 2 / Fragment: UNP residues 133-363 / Mutation: E45C, T54C, W184A, M185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B6DRA0, UniProt: P12493*PLUS
#3: Protein CA


Mass: 25618.439 Da / Num. of mol.: 2 / Fragment: UNP residues 107-337 / Mutation: A42C, W184A, M185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T2CI25, UniProt: P12493*PLUS
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.6 % / Description: hexagonal
Crystal growTemperature: 293 K / Method: microbatch / pH: 8
Details: 0.1 M PCB buffer, pH 8 (sodium propionate, sodium cacodylate, Bis-Tris propane), 25% w/v PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 17, 2016
RadiationMonochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.96→45 Å / Num. obs: 30532 / % possible obs: 92.5 % / Redundancy: 1.8 % / Biso Wilson estimate: 99.19 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.9
Reflection shellResolution: 2.96→3.01 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2873 / CC1/2: 0.351 / % possible all: 86.03

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000v715data reduction
HKL-2000v715data scaling
PHASER7.0.0phasing
Coot0.8.7model building
PHENIX1.12_2829refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3H47

3h47


Resolution: 2.96→45 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.925 / SU B: 27.261 / SU ML: 0.46 / Cross valid method: THROUGHOUT / ESU R Free: 0.48
RfactorNum. reflection% reflectionSelection details
Rfree0.26469 1471 4.8 %RANDOM
Rwork0.208 ---
obs0.21099 29060 92.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 103.954 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å23.98 Å21.86 Å2
2--0.42 Å22.73 Å2
3---2.45 Å2
Refinement stepCycle: 1 / Resolution: 2.96→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10061 0 6 3 10070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01310287
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179576
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.65313983
X-RAY DIFFRACTIONr_angle_other_deg1.1861.56722328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.33251290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55123.146499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.085151763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9171560
X-RAY DIFFRACTIONr_chiral_restr0.0580.21402
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211371
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021917
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it10.20811.1025196
X-RAY DIFFRACTIONr_mcbond_other10.20111.1015195
X-RAY DIFFRACTIONr_mcangle_it15.64516.6326474
X-RAY DIFFRACTIONr_mcangle_other15.64616.6346475
X-RAY DIFFRACTIONr_scbond_it9.36911.5655091
X-RAY DIFFRACTIONr_scbond_other9.36911.5665092
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.77517.1677510
X-RAY DIFFRACTIONr_long_range_B_refined19.99911496
X-RAY DIFFRACTIONr_long_range_B_other2011497
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A65640.06
12B65640.06
21A69440.01
22C69440.01
31A65870.06
32D65870.06
41A69160.01
42E69160.01
51A65830.06
52F65830.06
61B65640.06
62C65640.06
71B68120
72D68120
81B65780.06
82E65780.06
91B68090.01
92F68090.01
101C65820.06
102D65820.06
111C69180.01
112E69180.01
121C65860.06
122F65860.06
131D65660.06
132E65660.06
141D68300
142F68300
151E65660.06
152F65660.06
LS refinement shellResolution: 2.953→3.029 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 46 -
Rwork0.365 1999 -
obs--83.54 %

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