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- PDB-4lqw: Crystal structure of HIV-1 capsid N-terminal domain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4lqw
TitleCrystal structure of HIV-1 capsid N-terminal domain in complex with NUP358 cyclophilin
Components
  • Capsid protein p24
  • E3 SUMO-protein ligase RanBP2
KeywordsISOMERASE / cyclophilin / capsid
Function / homology
Function and homology information


cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / SUMO ligase activity / annulate lamellae / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein ...cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / SUMO ligase activity / annulate lamellae / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / Transferases; Acyltransferases; Aminoacyltransferases / SUMOylation of RNA binding proteins / nuclear export / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / SUMO transferase activity / nucleocytoplasmic transport / centrosome localization / Viral Messenger RNA Synthesis / regulation of gluconeogenesis / NLS-bearing protein import into nucleus / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / protein sumoylation / Regulation of HSF1-mediated heat shock response / mRNA transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / response to amphetamine / SUMOylation of chromatin organization proteins / GTPase activator activity / HCMV Late Events / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / ISG15 antiviral mechanism / small GTPase binding / host multivesicular body / DNA integration / HCMV Early Events / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / Separation of Sister Chromatids / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Signaling by ALK fusions and activated point mutants / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / protein folding / nuclear envelope / snRNP Assembly / symbiont-mediated suppression of host gene expression / viral nucleocapsid / nuclear membrane / 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 / intracellular membrane-bounded organelle / lipid binding / host cell nucleus / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / nucleoplasm / membrane / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Zinc finger domain ...Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Zinc finger domain / Cyclophilin-like / Cyclophilin / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / 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. / Tetratricopeptide-like helical domain superfamily / PH-like domain superfamily / 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 / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Gag-Pol polyprotein / E3 SUMO-protein ligase RanBP2
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPrice, A.J. / James, L.C.
CitationJournal: Retrovirology / Year: 2013
Title: HIV-1 capsid undergoes coupled binding and isomerization by the nuclear pore protein NUP358.
Authors: Bichel, K. / Price, A.J. / Schaller, T. / Towers, G.J. / Freund, S.M. / James, L.C.
History
DepositionJul 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Structure summary
Revision 1.2Sep 20, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 SUMO-protein ligase RanBP2
B: E3 SUMO-protein ligase RanBP2
C: Capsid protein p24
D: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)71,8364
Polymers71,8364
Non-polymers00
Water6,702372
1
A: E3 SUMO-protein ligase RanBP2
D: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)35,9182
Polymers35,9182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 SUMO-protein ligase RanBP2
C: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)35,9182
Polymers35,9182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.180, 38.260, 123.810
Angle α, β, γ (deg.)90.00, 100.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein E3 SUMO-protein ligase RanBP2 / 358 kDa nucleoporin / Nuclear pore complex protein Nup358 / Nucleoporin Nup358 / Ran-binding ...358 kDa nucleoporin / Nuclear pore complex protein Nup358 / Nucleoporin Nup358 / Ran-binding protein 2 / RanBP2 / p270 / Putative peptidyl-prolyl cis-trans isomerase / PPIase / Rotamase


Mass: 19713.320 Da / Num. of mol.: 2 / Fragment: UNP Residues 3057-3224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RANBP2, NUP358 / Production host: Escherichia coli (E. coli)
References: UniProt: P49792, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases), peptidylprolyl isomerase
#2: Protein Capsid protein p24 / CA


Mass: 16204.573 Da / Num. of mol.: 2 / Fragment: UNP Residues 133-278
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P12497
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 23 % v/v PEG 4000, 23 % glycerol, 8.5 % isopropanol, 85 mM HEPES pH 7.5, 20 mM spermine tetrahydrochloride, 100 mM glycine, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 1, 2009
RadiationMonochromator: DIAMOND(111) + Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.953→33.04 Å / Num. all: 48326 / Num. obs: 48326 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.953→2.004 Å / % possible all: 88.43

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1AK4

1ak4


Resolution: 1.95→33.04 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.305 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2465 2314 5.1 %RANDOM
Rwork0.20501 ---
obs0.20705 43143 94.04 %-
all-43143 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.506 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å2-0.13 Å2
2---0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.95→33.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4853 0 0 372 5225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0195013
X-RAY DIFFRACTIONr_bond_other_d0.0010.024794
X-RAY DIFFRACTIONr_angle_refined_deg0.8231.9446783
X-RAY DIFFRACTIONr_angle_other_deg0.66311063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.845634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82824.719231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.86415875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5941527
X-RAY DIFFRACTIONr_chiral_restr0.0480.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215716
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021151
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_it0.8852.3662509
X-RAY DIFFRACTIONr_mcbond_other0.8852.3652508
X-RAY DIFFRACTIONr_mcangle_it1.5253.983131
X-RAY DIFFRACTIONr_mcangle_other1.5253.9863132
X-RAY DIFFRACTIONr_scbond_it1.082.5622504
X-RAY DIFFRACTIONr_scbond_other1.0822.5662505
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8314.233646
X-RAY DIFFRACTIONr_long_range_B_refined3.94410.8245927
X-RAY DIFFRACTIONr_long_range_B_other3.77610.6935824
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.953→2.004 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 140 -
Rwork0.282 3009 -
obs--88.43 %
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)
10.43120.115-0.21250.67340.18291.20170.01410.00620.00420.0289-0.0638-0.01060.0108-0.08970.04970.0057-0.0026-0.00610.0119-0.00640.024118.7327-9.8984.3665
20.75770.13350.39480.14390.31730.75730.0167-0.02780.02050.0205-0.009-0.01060.0103-0.013-0.00770.0337-0.0048-0.00970.00890.00730.022845.68218.268223.8954
30.429-0.2547-0.27230.3608-0.15391.5340.0120.00780.0068-0.0222-0.0989-0.0040.01690.11960.08690.00170.00730.00130.04710.00490.018141.429-24.297857.6957
40.5541-0.06570.44070.2719-0.14780.81310.02290.0463-0.00180.01-0.05930.0363-0.01830.02070.03640.00510.00390.00090.0311-0.01440.024216.4469-5.429636.2381
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 173
2X-RAY DIFFRACTION2D1 - 144
3X-RAY DIFFRACTION3B2 - 173
4X-RAY DIFFRACTION4C1 - 144

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