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- PDB-6ec2: Structure of HIV-1 CA 1/3-hexamer -

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Basic information

Entry
Database: PDB / ID: 6ec2
TitleStructure of HIV-1 CA 1/3-hexamer
Components(Capsid protein p24) x 2
KeywordsVIRAL PROTEIN / capsid / disulfide
Function / homology
Function and homology information


Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cellular component / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / viral budding via host ESCRT complex ...Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cellular component / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / viral budding via host ESCRT complex / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / Membrane binding and targetting of GAG proteins / Assembly Of The HIV Virion / Budding and maturation of HIV virion / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / zinc ion binding / membrane
Similarity search - Function
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 / Retroviral matrix 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 / Retroviral matrix protein / Retrovirus capsid, C-terminal / 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
ACETATE ION / Gag polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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
DepositionAug 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.4Oct 23, 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: Capsid protein p24
C: Capsid protein p24
F: Capsid protein p24
G: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,1827
Polymers102,0054
Non-polymers1773
Water25214
1
A: Capsid protein p24
G: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0623
Polymers51,0022
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-17 kcal/mol
Surface area21340 Å2
MethodPISA
2
C: Capsid protein p24
F: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1214
Polymers51,0022
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-21 kcal/mol
Surface area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.800, 97.470, 150.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22F
13A
23G
14C
24F
15C
25G
16F
26G

NCS domain segments:

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

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CB
12AA
22FC
13AA
23GD
14CB
24FC
15CB
25GD
16FC
26GD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein Capsid protein p24 / Pr55Gag / HIV-1 CA 1/3-hexamer


Mass: 25457.217 Da / Num. of mol.: 2 / Mutation: E45C, T54E, W184A, M185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Gene: gag / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04591, UniProt: P12493*PLUS
#2: Protein Capsid protein p24 / Pr55Gag / HIV-1 CA 1/3-hexamer


Mass: 25545.279 Da / Num. of mol.: 2 / Mutation: A14C, A42E, W184A, M185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Gene: gag / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04591, UniProt: P12493*PLUS
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.7 Å3/Da / Density % sol: 54.38 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6
Details: 0.2M Calcium Acetate, 0.1 M MES:NaOH pH 6, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.4→50.01 Å / Num. obs: 28732 / % possible obs: 98.1 % / Redundancy: 2.1 % / CC1/2: 0.985 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.3
Reflection shellResolution: 3.4→3.49 Å / Rmerge(I) obs: 0.58 / Num. unique obs: 4449 / CC1/2: 0.739

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PHENIX1.12_2829refinement
XDS20180126data reduction
PHASER7.0.0phasing
Coot0.8.7model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 3H47

3h47


Resolution: 3.4→50.01 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.877 / SU B: 70.038 / SU ML: 0.49 / Cross valid method: THROUGHOUT / ESU R Free: 0.627
RfactorNum. reflection% reflectionSelection details
Rfree0.27505 806 5.2 %RANDOM
Rwork0.21071 ---
obs0.21407 14844 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 74.863 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å20 Å20 Å2
2--8.59 Å20 Å2
3----6.94 Å2
Refinement stepCycle: 1 / Resolution: 3.4→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6352 0 12 14 6378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196527
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.9628878
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3965824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58925.18278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.561151101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8491535
X-RAY DIFFRACTIONr_chiral_restr0.1230.21013
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214891
X-RAY DIFFRACTIONr_gen_planes_other
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_it4.2977.2543308
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.09110.8564114
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.3387.3313219
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined14.27666.6827629
X-RAY DIFFRACTIONr_long_range_B_other
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)
11A5080.1
12C5080.1
21A5400.17
22F5400.17
31A5160.14
32G5160.14
41C4940.13
42F4940.13
51C5160.11
52G5160.11
61F4960.16
62G4960.16
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 55 -
Rwork0.302 1067 -
obs--99.73 %
Refinement TLS params.Method: refined / Origin x: 11.0893 Å / Origin y: -14.3563 Å / Origin z: -24.3194 Å
111213212223313233
T0.0199 Å20.0027 Å2-0.0008 Å2-0.0109 Å20.0033 Å2--0.0165 Å2
L0.0196 °20.0208 °2-0.0004 °2-0.0761 °2-0.1213 °2--0.2855 °2
S-0.0043 Å °0.0104 Å °-0.0078 Å °0.0023 Å °0.0108 Å °-0.013 Å °-0.0053 Å °-0.0155 Å °-0.0065 Å °

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