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- PDB-3lry: Crystal structure of synthetic HIV-1 capsid C-terminal domain (CCA) -

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Basic information

Entry
Database: PDB / ID: 3lry
TitleCrystal structure of synthetic HIV-1 capsid C-terminal domain (CCA)
ComponentsHIV-1 capsid protein
KeywordsVIRAL PROTEIN / HIV-1 CAPSID / CORE PROTEIN / HIV / C-TERMINAL DOMAIN / AIDS
Function / homology
Function and homology information


viral process / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...viral process / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / viral capsid / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Retrovirus capsid C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal ...Retrovirus capsid C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Gag-Pol polyprotein / Gag protein
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsPazgier, M. / Lu, W.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Limitations of peptide retro-inverso isomerization in molecular mimicry.
Authors: Li, C. / Pazgier, M. / Li, J. / Li, C. / Liu, M. / Zou, G. / Li, Z. / Chen, J. / Tarasov, S.G. / Lu, W.Y. / Lu, W.
History
DepositionFeb 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 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 protein
B: HIV-1 capsid protein


Theoretical massNumber of molelcules
Total (without water)19,0622
Polymers19,0622
Non-polymers00
Water1,53185
1
A: HIV-1 capsid protein

A: HIV-1 capsid protein


Theoretical massNumber of molelcules
Total (without water)19,0622
Polymers19,0622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1470 Å2
ΔGint-12 kcal/mol
Surface area8080 Å2
MethodPISA
2
B: HIV-1 capsid protein

B: HIV-1 capsid protein


Theoretical massNumber of molelcules
Total (without water)19,0622
Polymers19,0622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1500 Å2
ΔGint-12 kcal/mol
Surface area8030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.907, 58.932, 58.732
Angle α, β, γ (deg.)90.000, 133.450, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 6 / Auth seq-ID: 150 - 219 / Label seq-ID: 5 - 74

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

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Components

#1: Protein HIV-1 capsid protein


Mass: 9530.921 Da / Num. of mol.: 2 / Fragment: C-terminal domain, dimerization domain / Source method: obtained synthetically / Source: (synth.) HUMAN IMMUNODEFICIENCY VIRUS 1 / References: UniProt: Q71B91, UniProt: P12497*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 0.8 M potassium phosphate monohydrate, 0.8M potassium phosphate monobasic, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.98→42.636 Å / Num. all: 14422 / Num. obs: 13819 / % possible obs: 96 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.065 / Rsym value: 0.068 / Net I/σ(I): 14.5
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2 / Num. unique all: 695 / Rsym value: 0.507 / % possible all: 95.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A43

1a43


Resolution: 1.98→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.281 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.269 624 5 %RANDOM
Rwork0.213 ---
obs0.216 12458 95.93 %-
all-11834 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 74.87 Å2 / Biso mean: 38.421 Å2 / Biso min: 28.64 Å2
Baniso -1Baniso -2Baniso -3
1-3.62 Å20 Å23.56 Å2
2---2.22 Å20 Å2
3---3.49 Å2
Refinement stepCycle: LAST / Resolution: 1.98→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1130 0 0 85 1215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221152
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.9831558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8335140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.82825.18554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26615216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.282158
X-RAY DIFFRACTIONr_chiral_restr0.110.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021864
X-RAY DIFFRACTIONr_mcbond_it0.9261.5712
X-RAY DIFFRACTIONr_mcangle_it1.64221152
X-RAY DIFFRACTIONr_scbond_it2.9483440
X-RAY DIFFRACTIONr_scangle_it5.0114.5406
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 560 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.255
LOOSE THERMAL1.0710
LS refinement shellResolution: 1.98→2.01 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 48 -
Rwork0.268 695 -
all-945 -
obs--95.6 %
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)
13.19392.56590.25198.36112.50574.667-0.03550.03620.16460.2607-0.1130.1078-0.0053-0.18180.14850.0423-0.0071-0.01330.16510.00820.0162-3.4580.49689.0443
23.00810.1762-0.59213.95691.23193.14260.05190.2115-0.0138-0.2093-0.04660.04430.1009-0.0857-0.00530.0690.00750.01580.16270.00570.029812.657115.675117.0427
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A149 - 219
2X-RAY DIFFRACTION2B149 - 219

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