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- PDB-5tsv: HIV-1 CA hexamer with NUP153 peptide - R3 crystal form -

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Basic information

Entry
Database: PDB / ID: 5tsv
TitleHIV-1 CA hexamer with NUP153 peptide - R3 crystal form
Components
  • HIV-1 CA protein
  • Nuclear pore complex protein Nup153
KeywordsVIRAL PROTEIN / viral capsid protein / hexamer / FG repeat
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 / 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 ...negative regulation of RNA export from nucleus / nuclear pore complex assembly / 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 / structural constituent of nuclear pore / nuclear localization sequence binding / 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 / mRNA transport / Regulation of HSF1-mediated heat shock response / nuclear pore / SUMOylation of DNA damage response and repair proteins / protein-membrane adaptor activity / nuclear periphery / SUMOylation of chromatin organization proteins / HCMV Late Events / Transcriptional regulation by small RNAs / molecular condensate scaffold activity / host multivesicular body / ISG15 antiviral mechanism / HCMV Early Events / viral penetration into host nucleus / protein import into nucleus / nuclear envelope / host cell / snRNP Assembly / nuclear membrane / viral nucleocapsid / amyloid fibril formation / viral translational frameshifting / symbiont entry into host cell / host cell nucleus / nucleolus / 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 / metal ion binding / 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
2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID / Gag polyprotein / Nuclear pore complex protein Nup153
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsSkorupka, K. / Ganser-Pornillos, B.K. / Pornillos, O.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI120956 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50-GM103297 United States
CitationJournal: To Be Published
Title: HIV-1 CA hexamer with NUP153 peptide - R3 crystal form
Authors: Skorupka, K. / Zadrozny, K. / Ganser-Pornillos, B.K. / Pornillos, O.
History
DepositionOct 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,4684
Polymers53,1363
Non-polymers3321
Water00
1
A: HIV-1 CA protein
B: HIV-1 CA protein
D: Nuclear pore complex protein Nup153
hetero molecules

A: HIV-1 CA protein
B: HIV-1 CA protein
D: Nuclear pore complex protein Nup153
hetero molecules

A: HIV-1 CA protein
B: HIV-1 CA protein
D: Nuclear pore complex protein Nup153
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,40412
Polymers159,4079
Non-polymers9973
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area20610 Å2
ΔGint-120 kcal/mol
Surface area60810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.924, 151.924, 69.646
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein HIV-1 CA protein / Pr55Gag


Mass: 25461.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate NY5)
Strain: isolate NY5 / Gene: gag / 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: 2213.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49790
#3: Chemical ChemComp-FLU / 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID / FLUORESCEIN


Mass: 332.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H12O5
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: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris, pH 8.2 12% PEG 8000 2% Tacsimate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 15603 / % possible obs: 75.3 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.5-2.541.50.4591.20.471123.7
2.54-2.591.60.3631.70.758128.3
2.59-2.641.70.4231.70.674134.3
2.64-2.691.80.4171.90.694139.3
2.69-2.751.90.35720.791147.1
2.96-3.052.50.2224.30.929177.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H47

3h47


Resolution: 2.502→47.824 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 28.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2512 1266 10.09 %
Rwork0.2035 --
obs0.2082 12545 60.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.502→47.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3390 0 25 0 3415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023493
X-RAY DIFFRACTIONf_angle_d0.4754752
X-RAY DIFFRACTIONf_dihedral_angle_d11.5062138
X-RAY DIFFRACTIONf_chiral_restr0.038532
X-RAY DIFFRACTIONf_plane_restr0.003619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5015-2.60170.3832230.3029190X-RAY DIFFRACTION9
2.6017-2.72010.3227520.313438X-RAY DIFFRACTION22
2.7201-2.86350.3086810.2849731X-RAY DIFFRACTION36
2.8635-3.04290.31921170.25771061X-RAY DIFFRACTION51
3.0429-3.27780.29591420.24841267X-RAY DIFFRACTION61
3.2778-3.60750.29071700.23331542X-RAY DIFFRACTION75
3.6075-4.12930.2532250.19381949X-RAY DIFFRACTION94
4.1293-5.20140.22132300.16352062X-RAY DIFFRACTION100
5.2014-47.83250.20122260.18352039X-RAY DIFFRACTION99
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)
10.0742-0.03440.07950.10240.04870.1734-0.02290.08460.0927-0.0699-0.046-0.0675-0.07150.0681-0.11770.02460.027-0.0150.10930.08760.061316.323919.0129-7.5528
20.0064-0.0013-0.00070.0188-0.00290.00220.0159-0.0601-0.02960.05230.003-0.03020.06720.02640.01130.16850.0376-0.16660.1309-0.01160.161137.46021.627414.8872
30.0285-0.01950.00610.20830.00260.00080.02810.0345-0.0033-0.0668-0.0301-0.14960.00240.03270.1043-0.036-0.01650.0241-0.01560.08920.085425.2696-4.5984-8.7669
40.00320.00230.00190.0005-0.00050.0002-0.0086-0.0276-0.04430.0074-0.0289-0.01510.02630.0598-0.03580.2194-0.0536-0.04520.31610.22730.310519.8618-32.16614.2514
50.0020.00560.0080.02720.01420.03520.0050.01110.0103-0.0058-0.0065-0.0063-0.0159-0.0088-0.00460.0820.00110.03160.18290.03480.261230.27849.2203-1.1694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 144 )
2X-RAY DIFFRACTION2chain 'A' and (resid 145 through 219 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 144 )
4X-RAY DIFFRACTION4chain 'B' and (resid 145 through 219 )
5X-RAY DIFFRACTION5chain 'D' and (resid 1410 through 1419 )

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