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- PDB-6eco: Hexamer-2-Foldon HIV-1 capsid platform -

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Basic information

Entry
Database: PDB / ID: 6eco
TitleHexamer-2-Foldon HIV-1 capsid platform
Components(HIV-1 capsid platform protein) x 2
KeywordsVIRAL PROTEIN / disulfide / capsid / template-driven polymerization
Function / homology
Function and homology information


host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / 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 ...host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / 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 / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / 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 / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / 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) / 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 ...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
Gag polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 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)5P50GM082251-12 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 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 capsid platform protein
D: HIV-1 capsid platform protein


Theoretical massNumber of molelcules
Total (without water)52,9182
Polymers52,9182
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Elutes at position consistent with trimer of dimers
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-16 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.250, 95.250, 122.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 1 - 221 / Label seq-ID: 1 - 221

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

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Components

#1: Protein HIV-1 capsid platform protein / Pr55Gag


Mass: 28129.178 Da / Num. of mol.: 1 / Mutation: E45C, T54E
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 HIV-1 capsid platform protein / Pr55Gag


Mass: 24788.379 Da / Num. of mol.: 1 / Mutation: A14C, A42E, A204D
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

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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: 3.03 Å3/Da / Density % sol: 59.45 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 0.2M Sodium Chloride, 0.1M HEPES pH 7.5, 12% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9798 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 4.2→50.01 Å / Num. obs: 8601 / % possible obs: 94.7 % / Redundancy: 3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.4
Reflection shellResolution: 4.2→4.31 Å / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.815

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDS20180126data scaling
XDS20180126data reduction
PHASER7.0.0phasing
Coot0.8.7model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XFX

4xfx


Resolution: 4.2→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 375.953 / SU ML: 2.393 / Cross valid method: THROUGHOUT / ESU R Free: 1.13
RfactorNum. reflection% reflectionSelection details
Rfree0.31638 214 4.4 %RANDOM
Rwork0.28637 ---
obs0.28766 4690 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 256.555 Å2
Baniso -1Baniso -2Baniso -3
1--12.68 Å2-6.34 Å20 Å2
2---12.68 Å20 Å2
3---41.15 Å2
Refinement stepCycle: 1 / Resolution: 4.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 0 0 3252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193323
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9594517
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6015422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.16624.926136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.46415551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0741518
X-RAY DIFFRACTIONr_chiral_restr0.0960.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212487
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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

Ens-ID: 1 / Number: 520 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2D
LS refinement shellResolution: 4.2→4.307 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 15 -
Rwork0.475 327 -
obs--97.71 %
Refinement TLS params.Method: refined / Origin x: 24.3138 Å / Origin y: 281.6923 Å / Origin z: 152.5298 Å
111213212223313233
T0.5844 Å2-0.156 Å2-0.4363 Å2-0.2116 Å2-0.1643 Å2--0.819 Å2
L1.7933 °2-0.4593 °2-1.3642 °2-3.2035 °2-1.4776 °2--2.1222 °2
S-0.2358 Å °0.0647 Å °-0.0569 Å °0.0259 Å °0.0966 Å °-0.1844 Å °0.2294 Å °-0.1382 Å °0.1392 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 221
2X-RAY DIFFRACTION1D148 - 221

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