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- PDB-9s6n: HIV-1 capsid (M-group) - Nup153 -

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Basic information

Entry
Database: PDB / ID: 9s6n
TitleHIV-1 capsid (M-group) - Nup153
Components
  • Gag polyprotein
  • Nuclear pore complex protein Nup153
KeywordsVIRAL PROTEIN / Hexameric HIV-1 (M-group)
Function / homology
Function and homology information


negative regulation of RNA export from nucleus / nuclear pore complex assembly / Nuclear Pore Complex (NPC) Disassembly / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / nuclear inclusion body / Transport of Ribonucleoproteins into the Host Nucleus / nuclear pore nuclear basket / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA ...negative regulation of RNA export from nucleus / nuclear pore complex assembly / Nuclear Pore Complex (NPC) Disassembly / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / nuclear inclusion body / Transport of Ribonucleoproteins into the Host Nucleus / nuclear pore nuclear basket / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / SUMOylation of SUMOylation proteins / structural constituent of nuclear pore / Transport of Mature mRNA Derived from an Intronless Transcript / NS1 Mediated Effects on Host Pathways / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / RNA export from nucleus / tRNA processing in the nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / nucleocytoplasmic transport / nuclear localization sequence binding / Viral Messenger RNA Synthesis / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / nuclear pore / Regulation of HSF1-mediated heat shock response / mRNA transport / SUMOylation of DNA damage response and repair proteins / protein-membrane adaptor activity / nuclear periphery / protein import into nucleus / SUMOylation of chromatin organization proteins / HCMV Late Events / molecular condensate scaffold activity / viral penetration into host nucleus / host multivesicular body / ISG15 antiviral mechanism / HCMV Early Events / nuclear envelope / host cell / nuclear membrane / viral nucleocapsid / snRNP Assembly / amyloid fibril formation / viral translational frameshifting / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / structural molecule activity / DNA binding / RNA binding / nucleoplasm / zinc ion binding / ATP binding / membrane / identical protein binding
Similarity search - Function
Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. ...Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / : / 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 / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
IODIDE ION / Gag polyprotein / Nuclear pore complex protein Nup153
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGovasli, M.A.L. / Pinotsis, N. / Towers, G. / Selwood, D. / Jacques, D.A.
Funding support United Kingdom, European Union, Australia, 4items
OrganizationGrant numberCountry
Wellcome Trust220863 United Kingdom
Wellcome Trust214344 United Kingdom
European Research Council (ERC)339223European Union
National Health and Medical Research Council (NHMRC, Australia)GNT2013215 Australia
CitationJournal: To Be Published
Title: Cofactor-mimicking HIV-1 capsid inhibitors, and their escape mutants, drive innate immune sensing
Authors: Govasli, M.A.L. / Pinotsis, N. / Towers, G. / Selwood, D. / Jacques, D.A.
History
DepositionAug 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gag polyprotein
B: Nuclear pore complex protein Nup153
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6436
Polymers27,3182
Non-polymers3254
Water30617
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-20 kcal/mol
Surface area13830 Å2
Unit cell
Length a, b, c (Å)92.281, 92.281, 58.483
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Space group name HallP6
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z

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Components

#1: Protein Gag polyprotein


Mass: 25630.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B6DRA0
#2: Protein/peptide Nuclear pore complex protein Nup153 / 153 kDa nucleoporin / Nucleoporin Nup153


Mass: 1687.721 Da / Num. of mol.: 1 / Fragment: UNP residues 1407-1423 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49790
#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9.5-11% PEG 3350 (v/v), 250-350 mM NaI, 100 mM Sodium Cacodylate [pH 6.5]. Crystals grew in 1 uL protein (3 mg/mL) + 1 uL crystallant. Cryoprotected in 20% (v/v) Glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Mar 11, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.6→36.22 Å / Num. obs: 8576 / % possible obs: 98.1 % / Redundancy: 4 % / Biso Wilson estimate: 72.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.4
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4253 / CC1/2: 0.898

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSJan 10, 2022 BUILT=20220220data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→36.22 Å / SU ML: 0.4225 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.8931
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2865 422 4.92 %
Rwork0.2529 8154 -
obs0.2548 8576 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.71 Å2
Refinement stepCycle: LAST / Resolution: 2.6→36.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 4 17 1787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011817
X-RAY DIFFRACTIONf_angle_d1.23492472
X-RAY DIFFRACTIONf_chiral_restr0.0622276
X-RAY DIFFRACTIONf_plane_restr0.0112323
X-RAY DIFFRACTIONf_dihedral_angle_d5.9479243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.980.37251390.37462750X-RAY DIFFRACTION98.77
2.98-3.750.34121520.30882704X-RAY DIFFRACTION97.37
3.75-36.220.24841310.21282700X-RAY DIFFRACTION94.62
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)
17.147653413531.430100483482.318991342346.764108618481.139406949075.48326897556-0.321751110592-0.01507857075130.390307232132-0.7316383865090.01590733464810.642711918998-0.2901124141650.197708974420.3786467779590.4626085992450.00206810043368-0.0900001510140.483266766135-0.08136333159640.956760691704-15.1182726652-8.7503632478-4.0464164007
21.175406947350.8882958137573.265319492755.606412379122.54319815569.02833502611-0.0672237453810.615045991189-0.574474821439-0.9379428757030.2645590814740.0910987326677-0.3084804313650.0578456682184-0.2394446764480.61331064163-0.05534320822990.1004969983580.776927847873-0.282127112111.23178775076-25.5867591417-17.9711807168-13.1153304378
32.20166431897-2.56059609637-2.298115339057.401546621561.208396333763.94948749791-0.245262273619-1.577828101460.8551885615730.4194426104530.229080207653-1.42477576563-0.07878636159180.893845316181-0.1424550408340.237923191630.3335849859230.0488951906291.42576969643-0.03421675507350.565697491031-34.14571438285.3172288565615.0411618764
43.144287246933.11275248175-0.8844001011145.433383571612.558676905375.182085073430.759953799990.1849176918291.655723956910.0665682699533-0.6167413114850.299538560109-1.15075220574-1.22202135315-0.2133310110160.9143927623060.4118874044910.1272429286721.00044863207-0.005157459500151.02615260176-41.320875526512.342813776710.1491337856
53.24906351063-0.426584447241-1.647103999222.720331257681.579649979931.53438309899-0.749172693283-0.18584435873-0.426439392251-0.5544935392320.4855335566080.1554833310340.6374598488440.6631663292670.4706189113550.696992237080.0293715038354-0.03916747575380.8088104744430.1108356186710.642524018666-14.4240871908-29.3140686514-1.87146461266
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 63 )AA1 - 631 - 63
22chain 'A' and (resid 64 through 145 )AA64 - 14564 - 145
33chain 'A' and (resid 146 through 175 )AA146 - 175146 - 175
44chain 'A' and (resid 176 through 219 )AA176 - 219176 - 219
55chain 'B' and (resid 1409 through 1418 )BF1409 - 14181 - 10

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