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- PDB-6ecn: HIV-1 CA 1/2-hexamer-EE -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6ecn
TitleHIV-1 CA 1/2-hexamer-EE
Components(HIV-1 CA) x 3
KeywordsVIRAL PROTEIN / disulfide crosslink / capsid
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 / viral process / Assembly Of The HIV Virion / Budding and maturation of HIV virion / ISG15 antiviral mechanism / host multivesicular body / viral capsid / viral nucleocapsid / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / zinc ion binding / membrane
Similarity search - Function
Retroviral nucleocapsid Gag protein p24, N-terminal / 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) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain ...Retroviral nucleocapsid Gag protein p24, N-terminal / 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) / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Gag protein / Gag polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Human immunodeficiency virus
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)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 1.0Aug 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 CA
B: HIV-1 CA
C: HIV-1 CA
D: HIV-1 CA
E: HIV-1 CA
F: HIV-1 CA


Theoretical massNumber of molelcules
Total (without water)135,2236
Polymers135,2236
Non-polymers00
Water00
1
A: HIV-1 CA
B: HIV-1 CA
C: HIV-1 CA


Theoretical massNumber of molelcules
Total (without water)67,6123
Polymers67,6123
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-35 kcal/mol
Surface area27370 Å2
MethodPISA
2
D: HIV-1 CA
E: HIV-1 CA
F: HIV-1 CA


Theoretical massNumber of molelcules
Total (without water)67,6123
Polymers67,6123
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-32 kcal/mol
Surface area27140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.600, 84.100, 248.550
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
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 - 2191 - 219
21GLNGLNBB1 - 2191 - 219
12SERSERAA1 - 1461 - 146
22SERSERCC1 - 1461 - 146
13GLNGLNAA1 - 2191 - 219
23GLNGLNDD1 - 2191 - 219
14CYSCYSAA1 - 2181 - 218
24CYSCYSEE1 - 2181 - 218
15SERSERAA1 - 1461 - 146
25SERSERFF1 - 1461 - 146
16SERSERBB1 - 1461 - 146
26SERSERCC1 - 1461 - 146
17GLNGLNBB1 - 2191 - 219
27GLNGLNDD1 - 2191 - 219
18CYSCYSBB1 - 2181 - 218
28CYSCYSEE1 - 2181 - 218
19SERSERBB1 - 1461 - 146
29SERSERFF1 - 1461 - 146
110SERSERCC1 - 1461 - 146
210SERSERDD1 - 1461 - 146
111SERSERCC1 - 1461 - 146
211SERSEREE1 - 1461 - 146
112LYSLYSCC1 - 1471 - 147
212LYSLYSFF1 - 1471 - 147
113CYSCYSDD1 - 2181 - 218
213CYSCYSEE1 - 2181 - 218
114SERSERDD1 - 1461 - 146
214SERSERFF1 - 1461 - 146
115SERSEREE1 - 1461 - 146
215SERSERFF1 - 1461 - 146

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 HIV-1 CA / Pr55Gag


Mass: 25431.246 Da / Num. of mol.: 2 / 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) / Strain (production host): BL21(DE3) / References: UniProt: P04591, UniProt: P12493*PLUS
#2: Protein HIV-1 CA / Pr55Gag


Mass: 25515.254 Da / Num. of mol.: 2 / Mutation: A42C, T54E, W184A, M185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus / Gene: gag / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04591, UniProt: P12493*PLUS
#3: Protein HIV-1 CA


Mass: 16665.143 Da / Num. of mol.: 2 / Mutation: A14C, A42E
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) / Strain (production host): BL21(DE3) / References: UniProt: A0A248SME6, 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: 2.54 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 293 K / Method: microbatch / Details: 0.1M Sodium Citrate pH 5, 8% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.4→50.1 Å / Num. obs: 36208 / % possible obs: 99 % / Redundancy: 3.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.7
Reflection shellResolution: 3.4→3.49 Å / Rmerge(I) obs: 1.1 / CC1/2: 0.628

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDS20180126data scaling
XDS20180126data reduction
PHASER7.0.0phasing
Coot0.8.7model building
PHENIX1.12-2829refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H47

3h47


Resolution: 3.4→50.01 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / SU B: 105.087 / SU ML: 0.68 / Cross valid method: THROUGHOUT / ESU R Free: 0.637
RfactorNum. reflection% reflectionSelection details
Rfree0.27533 955 4.9 %RANDOM
Rwork0.22535 ---
obs0.22789 18699 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 143.303 Å2
Baniso -1Baniso -2Baniso -3
1-10.42 Å20 Å20 Å2
2---1.79 Å20 Å2
3----8.63 Å2
Refinement stepCycle: 1 / Resolution: 3.4→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8369 0 0 0 8369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198551
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.95711631
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.50151084
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3625.057348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.172151406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0931543
X-RAY DIFFRACTIONr_chiral_restr0.1030.21331
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216370
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_it4.7677.8264387
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.10111.725454
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.8628.0564164
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined16.70872.67535959
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)
11A5160.13
12B5160.13
21A3580.16
22C3580.16
31A5380.11
32D5380.11
41A5180.15
42E5180.15
51A3460.17
52F3460.17
61B3420.16
62C3420.16
71B5340.14
72D5340.14
81B5260.14
82E5260.14
91B3400.16
92F3400.16
101C3600.1
102D3600.1
111C3400.17
112E3400.17
121C3760.06
122F3760.06
131D5220.13
132E5220.13
141D3540.11
142F3540.11
151E3320.16
152F3320.16
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 66 -
Rwork0.378 1359 -
obs--99.86 %
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)
13.50740.91551.57611.96231.97012.18410.4281-0.25760.3805-0.0054-0.77920.26180.0852-0.5990.35111.1049-0.1127-0.10960.7956-0.20540.4547-6.9519-6.8775-59.523
20.8738-0.94470.60541.0729-0.28855.3107-0.04950.08460.30380.1015-0.1033-0.24550.03780.2470.15270.9576-0.2343-0.06870.877-0.00760.465215.7506-4.8632-87.9297
30.0625-0.10620.28870.2131-0.53482.8577-0.13640.10090.02460.099-0.4598-0.08840.3548-0.37810.59621.6358-0.6382-0.14760.9827-0.25390.345-12.0313-20.8974-39.4481
43.10760.93131.12411.39950.60125.4539-0.177-0.20210.0971-0.2663-0.1464-0.0626-0.11920.45130.32340.9291-0.069-0.08280.65040.0060.515815.7689-0.042-49.4951
52.91510.09660.55942.538-0.84364.03770.01970.22650.00180.34840.11350.0332-0.20230.2078-0.13330.9292-0.047-0.08580.537-0.05710.5251-8.4305-15.6053-83.275
63.33-0.98310.18411.2320.39682.9291-0.1638-0.1854-0.0412-0.17710.3475-0.22490.0407-0.048-0.18370.91980.0242-0.08910.5451-0.03980.595929.6497-3.1072-11.9807
71.38230.6498-0.91470.7781.32477.6417-0.1851-0.06510.3704-0.271-0.07820.206-0.1033-0.07640.26330.90420.1534-0.0180.6227-0.18150.651512.920625.41214.2553
81.4159-0.69860.58681.9933-2.93074.48990.6917-0.4559-0.2801-1.050.15390.57961.4126-0.0214-0.84561.5352-0.1146-0.55980.32010.08280.512521.466-25.7763-20.1588
90.5547-0.62351.43322.11330.10845.8786-0.1018-0.1744-0.00450.05520.2888-0.1723-0.2613-0.532-0.1870.97080.0331-0.08870.59230.02120.600112.93297.596-29.4718
102.0481-0.041.29023.25790.85783.20510.4924-0.38140.2585-0.0469-0.3826-0.22030.3502-0.6702-0.10980.9877-0.0721-0.10410.67550.04330.392325.93364.106713.0321
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 147
2X-RAY DIFFRACTION2A148 - 219
3X-RAY DIFFRACTION3B1 - 147
4X-RAY DIFFRACTION4B148 - 219
5X-RAY DIFFRACTION5C1 - 147
6X-RAY DIFFRACTION6D1 - 147
7X-RAY DIFFRACTION7D148 - 219
8X-RAY DIFFRACTION8E1 - 147
9X-RAY DIFFRACTION9E148 - 219
10X-RAY DIFFRACTION10F1 - 147

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