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- PDB-3nte: Crystal Structure of the Wild-type Full-Length HIV-1 Capsid Protein -

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Basic information

Entry
Database: PDB / ID: 3nte
TitleCrystal Structure of the Wild-type Full-Length HIV-1 Capsid Protein
ComponentsHIV-1 capsid protein
KeywordsVIRAL PROTEIN / wild type viral protein
Function / homology
Function and homology information


positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity / positive regulation of calcidiol 1-monooxygenase activity / ATP biosynthetic process / viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / host cell nucleus / structural molecule activity / RNA binding / zinc ion binding ...positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity / positive regulation of calcidiol 1-monooxygenase activity / ATP biosynthetic process / viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / host cell nucleus / structural molecule activity / RNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Retroviral nucleocapsid Gag protein p24, N-terminal / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) ...Retroviral nucleocapsid Gag protein p24, N-terminal / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / 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 / 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
: / Tri-iodode Anion / IODIDE ION / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBetts, L. / Yeh, J.I.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structure of the HIV-1 full-length capsid protein in a conformationally trapped unassembled state induced by small-molecule binding.
Authors: Du, S. / Betts, L. / Yang, R. / Shi, H. / Concel, J. / Ahn, J. / Aiken, C. / Zhang, P. / Yeh, J.I.
History
DepositionJul 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 2, 2014Group: Database references
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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 protein
B: HIV-1 capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,48745
Polymers49,2602
Non-polymers4,22643
Water4,053225
1
A: HIV-1 capsid protein
hetero molecules

B: HIV-1 capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,48745
Polymers49,2602
Non-polymers4,22643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y+1/2,-z1
Buried area8100 Å2
ΔGint-268 kcal/mol
Surface area22870 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-251 kcal/mol
Surface area23070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.910, 86.532, 55.589
Angle α, β, γ (deg.)90.000, 99.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein HIV-1 capsid protein


Mass: 24630.225 Da / Num. of mol.: 2 / Fragment: UNP residues 133-353
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: HIV-1 / Gene: CA, gag / Production host: Escherichia coli (E. coli) / References: UniProt: Q77YG1

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Non-polymers , 5 types, 268 molecules

#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-I3M / Tri-iodode Anion


Mass: 380.713 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I3
#4: Chemical...
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.31 Å3/Da / Density % sol: 46.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9-12% PEG 3350, 0.2 M sodium iodide, 0.1 M Bis-Tris-propane pH 6.5, 0.01 M iron(III) chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 31847 / % possible obs: 97.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.064 / Χ2: 1.583 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-2.022.90.50127061.086182.4
2.02-2.13.20.3730211.133192.4
2.1-2.23.60.29731901.123198.3
2.2-2.313.80.22532421.261199.6
2.31-2.463.90.16632471.15199.9
2.46-2.6540.12332761.3151100
2.65-2.9140.08832751.5591100
2.91-3.333.90.05832641.8151100
3.33-4.23.90.03933022.0181100
4.2-503.70.0433243.026199.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6.1_336refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1ak4, 1a43

1ak4

1a43


Resolution: 1.95→29.048 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7825 / SU ML: 0.27 / Cross valid method: R-free / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2534 1578 5.08 %random
Rwork0.2037 ---
obs0.2064 31042 94.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.751 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso max: 91.12 Å2 / Biso mean: 36.4093 Å2 / Biso min: 14.75 Å2
Baniso -1Baniso -2Baniso -3
1-3.9374 Å20 Å2-8.4888 Å2
2---5.9086 Å2-0 Å2
3---1.9712 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3412 0 47 225 3684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083539
X-RAY DIFFRACTIONf_angle_d1.0934811
X-RAY DIFFRACTIONf_chiral_restr0.072543
X-RAY DIFFRACTIONf_plane_restr0.006627
X-RAY DIFFRACTIONf_dihedral_angle_d16.6491345
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.01720.31861230.26442255237872
2.0172-2.0980.29581340.24482621275584
2.098-2.19340.28261520.24112934308695
2.1934-2.3090.33131410.2393048318998
2.309-2.45360.25571650.222630813246100
2.4536-2.64290.25641580.215331233281100
2.6429-2.90870.30181640.218231023266100
2.9087-3.3290.2721810.214430793260100
3.329-4.19220.20311780.165131243302100
4.1922-29.05150.23151820.17863097327999
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)
10.9039-0.2517-0.17931.72080.5952.0521-0.0611-0.0732-0.04540.0213-0.03860.17020.217-0.064500.1672-0.02940.02790.1776-0.02280.2188-32.5284-8.193412.337
21.00750.70730.31910.31450.64490.9566-0.11890.16220.1716-0.34720.13260.045-0.09230.1109-00.2679-0.0194-0.02730.32810.01440.3313-45.225919.4149-10.533
32.31210.9593-0.05411.738-0.73492.0591-0.03330.1040.16590.16820.028-0.0177-0.2437-0.063300.15380.04220.00440.1046-0.0190.1152-31.900136.92565.5124
40.75010.0485-0.03980.50130.36411.0969-0.12-0.05930.15470.1557-0.032-0.07010.01750.085800.2891-0.0136-0.0060.2390.00380.1998-20.50876.76728.7669
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and ((resseq 1:142))B0
2X-RAY DIFFRACTION2chain 'B' and ((resseq 143:225))B0
3X-RAY DIFFRACTION3chain 'A' and ((resseq 1:142))A0
4X-RAY DIFFRACTION4chain 'A' and ((resseq 146:221))A0

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