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- PDB-6aya: Structure of the native full-length HIV-1 capsid protein in compl... -

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Basic information

Entry
Database: PDB / ID: 6aya
TitleStructure of the native full-length HIV-1 capsid protein in complex with Nup153 peptide
Components
  • HIV-1 capsid protein
  • Nuclear pore complex protein Nup153
KeywordsVIRAL PROTEIN / HIV-1 capsid protein / hexamer / Nup153 complex
Function / homology
Function and homology information


negative regulation of RNA export from nucleus / nuclear pore complex assembly / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / 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 / nuclear inclusion body / nuclear pore nuclear basket / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / nuclear localization sequence binding / structural constituent of nuclear pore / Transport of Mature mRNA Derived from an Intronless Transcript / 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 / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA export from nucleus / tRNA processing in the nucleus / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / viral budding via host ESCRT complex / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA transport / nuclear pore / SUMOylation of DNA damage response and repair proteins / protein-membrane adaptor activity / nuclear periphery / SUMOylation of chromatin organization proteins / HCMV Late Events / molecular condensate scaffold activity / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / viral penetration into host nucleus / host multivesicular body / protein import into nucleus / HCMV Early Events / nuclear envelope / host cell / viral nucleocapsid / snRNP Assembly / nuclear membrane / amyloid fibril formation / viral translational frameshifting / symbiont entry into host cell / nucleolus / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / membrane / cytosol
Similarity search - Function
Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Zinc finger domain / Gag protein p6 ...Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Zinc finger domain / Gag protein p6 / Gag protein p6 / 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 / 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 / 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 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
IODIDE ION / Gag polyprotein / Nuclear pore complex protein Nup153
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsGres, A.T. / Kirby, K.A. / Sarafianos, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI120860 United States
CitationJournal: Nat Commun / Year: 2023
Title: Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization.
Authors: Gres, A.T. / Kirby, K.A. / McFadden, W.M. / Du, H. / Liu, D. / Xu, C. / Bryer, A.J. / Perilla, J.R. / Shi, J. / Aiken, C. / Fu, X. / Zhang, P. / Francis, A.C. / Melikyan, G.B. / Sarafianos, S.G.
History
DepositionSep 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_initial_refinement_model
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 capsid protein
B: Nuclear pore complex protein Nup153
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,27711
Polymers27,3182
Non-polymers9599
Water99155
1
A: HIV-1 capsid protein
B: Nuclear pore complex protein Nup153
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)169,66466
Polymers163,90912
Non-polymers5,75554
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area32180 Å2
ΔGint-268 kcal/mol
Surface area59680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.544, 92.544, 58.288
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

#1: Protein HIV-1 capsid protein


Mass: 25630.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL4-3 / Gene: Gag-pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12493
#2: Protein/peptide Nuclear pore complex protein Nup153 / 153 kDa nucleoporin / Nucleoporin Nup153


Mass: 1687.721 Da / Num. of mol.: 1 / 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.: 7 / 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.: 55 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 53.37 % / Mosaicity: 0.17 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350, NaI, MIB, Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.000031 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000031 Å / Relative weight: 1
ReflectionResolution: 2.4→36.241 Å / Num. obs: 10941 / % possible obs: 97.2 % / Redundancy: 10.6 % / Biso Wilson estimate: 51.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.021 / Rrim(I) all: 0.068 / Net I/σ(I): 24.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.4-2.4910.80.68911680.9010.220.723100
8.98-36.249.80.0322200.9980.0110.03494.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.31 Å36.24 Å
Translation2.31 Å36.24 Å

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
Blu-Icedata collection
PHENIX1.11.1-2575_1692refinement
PDB_EXTRACT3.22data extraction
Aimless0.5.32data reduction
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XFX

4xfx


Resolution: 2.4→36.241 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.58
RfactorNum. reflection% reflection
Rfree0.2736 630 5.77 %
Rwork0.2336 --
obs0.2358 10924 97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 191.38 Å2 / Biso mean: 71.3651 Å2 / Biso min: 25.54 Å2
Refinement stepCycle: final / Resolution: 2.4→36.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1739 0 9 55 1803
Biso mean--79.67 59.84 -
Num. residues----223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021784
X-RAY DIFFRACTIONf_angle_d0.5082425
X-RAY DIFFRACTIONf_chiral_restr0.04271
X-RAY DIFFRACTIONf_plane_restr0.005314
X-RAY DIFFRACTIONf_dihedral_angle_d11.5151093
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4002-2.64160.35481490.292726372786100
2.6416-3.02370.33551580.288526342792100
3.0237-3.80890.30921580.25432465262393
3.8089-36.24490.22761650.19962558272395
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)
10.3376-0.65030.47151.3479-0.62062.50460.73990.21280.2065-0.46550.59060.26350.1033-0.15490.86320.80810.00830.21450.41580.06080.1764-1.4984-12.406715.0075
20.29990.29850.08410.22320.18310.4512-0.02230.32020.1512-0.228-0.3491-0.4112-0.29230.4089-0.00030.30360.00130.01490.36630.09160.52842.7214-17.0698-3.2978
30.207-0.8409-0.36361.42980.57740.8839-0.28620.0793-0.33170.13740.08230.55030.0340.1822-0.02720.3808-0.02130.06350.24560.05690.4443-3.5289-29.60453.7124
43.2524-0.02792.3266-0.0345-0.0951.711-0.4715-1.43520.46360.3013-0.2467-0.5252-0.5098-0.387-0.47860.8863-0.06750.25240.23190.29460.3971-7.4279-33.859822.9641
52.5103-0.4154-0.88362.8784-1.05752.05040.0040.31-0.41250.44850.01650.7208-0.1387-0.46340.07740.35110.05120.09320.25470.02870.34735.4051-27.72092.6619
60.69210.49960.52170.54050.52580.4967-0.0401-0.11690.3492-0.30480.0384-0.27680.27310.2569-0.00160.4910.1925-0.00170.42530.06890.352823.5438-29.8838-9.8834
70.51740.6860.19181.38090.23522.6878-0.7725-0.29550.3771-0.15230.2288-0.0081.40311.961-0.05780.38740.2196-0.10351.17-0.09280.595935.8591-25.6943-14.3873
80.35790.2313-0.18860.2339-0.05940.09030.07460.1628-0.3810.2341-0.02380.0395-0.4288-0.82380.00140.7102-0.01490.08141.3261-0.2360.6068-16.3441-26.731.0094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )A1 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 44 )A17 - 44
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 83 )A45 - 83
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 105 )A84 - 105
5X-RAY DIFFRACTION5chain 'A' and (resid 106 through 160 )A106 - 160
6X-RAY DIFFRACTION6chain 'A' and (resid 161 through 192 )A161 - 192
7X-RAY DIFFRACTION7chain 'A' and (resid 193 through 219 )A193 - 219
8X-RAY DIFFRACTION8chain 'B' and (resid 1410 through 1418 )B0

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