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- PDB-6ay9: Structure of the native full-length HIV-1 capsid protein in compl... -

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Basic information

Entry
Database: PDB / ID: 6ay9
TitleStructure of the native full-length HIV-1 capsid protein in complex with CPSF6 peptide
Components
  • Cleavage and polyadenylation specificity factor subunit 6
  • HIV-1 capsid protein
KeywordsVIRAL PROTEIN / HIV-1 capsid protein / hexamer / CPSF6 complex
Function / homology
Function and homology information


exon-exon junction complex binding / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / interchromatin granule / Processing of Intronless Pre-mRNAs / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / mRNA 3'-end processing ...exon-exon junction complex binding / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / interchromatin granule / Processing of Intronless Pre-mRNAs / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / mRNA 3'-end processing / Signaling by cytosolic FGFR1 fusion mutants / mRNA 3'-end processing / paraspeckles / RNA Polymerase II Transcription Termination / protein heterotetramerization / viral budding via host ESCRT complex / ribosomal large subunit binding / Processing of Capped Intron-Containing Pre-mRNA / Signaling by FGFR1 in disease / protein tetramerization / ISG15 antiviral mechanism / host multivesicular body / mRNA processing / viral nucleocapsid / nuclear speck / ribonucleoprotein complex / viral translational frameshifting / mRNA binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / membrane / cytoplasm
Similarity search - Function
Cleavage and polyadenylation specificity factor subunit 6 / CPSF6/7 family / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / : / gag protein p24 N-terminal domain ...Cleavage and polyadenylation specificity factor subunit 6 / CPSF6/7 family / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / : / gag protein p24 N-terminal domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / 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. / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / Gag polyprotein / Gag polyprotein / Cleavage and polyadenylation specificity factor subunit 6
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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 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 capsid protein
B: Cleavage and polyadenylation specificity factor subunit 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,81712
Polymers26,9142
Non-polymers90310
Water55831
1
A: HIV-1 capsid protein
B: Cleavage and polyadenylation specificity factor subunit 6
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)166,90372
Polymers161,48312
Non-polymers5,41960
Water1086
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 area34350 Å2
ΔGint-410 kcal/mol
Surface area60640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.675, 92.675, 58.042
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 / Fragment: UNP residues 133-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B6DRA0, UniProt: P12493*PLUS
#2: Protein/peptide Cleavage and polyadenylation specificity factor subunit 6 / Cleavage and polyadenylation specificity factor 68 kDa subunit / CPSF 68 kDa subunit / Pre-mRNA ...Cleavage and polyadenylation specificity factor 68 kDa subunit / CPSF 68 kDa subunit / Pre-mRNA cleavage factor Im 68 kDa subunit / Protein HPBRII-4/7


Mass: 1283.472 Da / Num. of mol.: 1 / Fragment: UNP residues 276-287 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16630
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.67 Å3/Da / Density % sol: 53.99 % / Mosaicity: 0.13 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350, NaI, Sodium cacodylate, Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033203 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033203 Å / Relative weight: 1
ReflectionResolution: 2.5→47.03 Å / Num. obs: 9956 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 60.78 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.029 / Rrim(I) all: 0.069 / Net I/σ(I): 18.1 / Num. measured all: 55693 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.5-2.65.50.711190.5830.3260.774100
9.01-47.035.40.0332330.9980.0170.03799.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.43 Å47.03 Å
Translation5.43 Å47.03 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: 2.5→47.03 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 29.59
RfactorNum. reflection% reflection
Rfree0.2727 598 6.01 %
Rwork0.2421 --
obs0.2438 9950 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 170.31 Å2 / Biso mean: 75.0984 Å2 / Biso min: 31.27 Å2
Refinement stepCycle: final / Resolution: 2.5→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 10 31 1832
Biso mean--97.14 62.36 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021839
X-RAY DIFFRACTIONf_angle_d0.4962501
X-RAY DIFFRACTIONf_chiral_restr0.038277
X-RAY DIFFRACTIONf_plane_restr0.004326
X-RAY DIFFRACTIONf_dihedral_angle_d13.3531128
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5002-2.75180.37321670.356122952462
2.7518-3.14990.32171810.291322842465
3.1499-3.96820.26061230.235923562479
3.9682-47.04030.23911270.216424172544
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)
10.0209-0.0141-0.0459-0.0278-0.0120.0220.4175-0.6137-0.8784-0.1450.07930.3871-0.01650.3877-00.6082-0.10770.02970.57890.15160.4241-0.8425-12.32916.425
20.05450.1679-0.08980.14060.2230.0798-0.03550.03680.496-0.09580.0277-0.6334-0.01950.0248-00.3889-0.04610.09260.40550.02720.47442.6861-16.8541-3.5367
3-0.1222-0.52770.03650.49110.16280.5186-0.0978-0.0935-0.09730.06610.0843-0.08370.09950.232100.377-0.02190.05790.33350.08160.409-3.0178-29.41713.9272
4-0.00910.1059-0.01510.0034-0.05690.015-0.2041-0.19-0.2595-0.2422-0.6090.32980.03680.1919-00.7638-0.07670.24260.4560.09980.7701-6.9677-34.09823.4212
50.04940.1563-0.14240.1575-0.07720.13410.0309-0.72110.52990.6430.36231.1255-0.07960.0322-00.8840.08920.25450.6774-0.11780.6967-4.6858-24.418919.5162
60.08920.11260.00440.3069-0.18050.0586-0.083-0.0772-0.14630.2413-0.1395-0.41750.2702-0.075300.3311-0.01260.0530.46130.06680.56994.055-29.70513.3586
7-0.04740.01650.12930.20950.28030.3487-0.15470.24020.4173-0.50980.21150.36960.3029-0.209700.76940.2009-0.07760.63890.06220.439820.413-29.1626-18.8508
80.10550.12760.2264-0.01830.07630.16960.6525-0.7670.81830.3643-2.33141.46351.2063-1.511300.10770.7411-0.248-0.33750.81140.233722.4013-24.373-12.9681
90.0380.1032-0.02560.3250.01110.0924-0.0802-0.20430.3353-0.31320.0496-0.08570.66080.180100.48380.0830.00160.41980.06580.362524.5689-34.7574-6.7743
10-0.00310.03290.00930.0080.02620.0268-0.34050.3289-0.0039-0.1985-0.1563-0.3320.27210.21700.55120.1672-0.02810.9681-0.04810.833636.2604-28.673-18.2179
110.0293-0.0379-0.10030.00590.1340.1148-0.5152-0.36110.182-0.05130.2012-0.37160.47531.089-00.54830.05820.05880.74530.12880.789735.832-21.8359-11.3324
12-0.01330.0536-0.0017-0.00860.03480.024-0.1933-0.71-0.04920.3033-0.44520.04020.0894-0.6215-00.3678-0.15540.1110.66150.01830.1538-11.9718-31.86723.1623
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 43 )A17 - 43
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 83 )A44 - 83
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 104 )A84 - 104
5X-RAY DIFFRACTION5chain 'A' and (resid 105 through 125 )A105 - 125
6X-RAY DIFFRACTION6chain 'A' and (resid 126 through 144 )A126 - 144
7X-RAY DIFFRACTION7chain 'A' and (resid 145 through 160 )A145 - 160
8X-RAY DIFFRACTION8chain 'A' and (resid 161 through 174 )A161 - 174
9X-RAY DIFFRACTION9chain 'A' and (resid 175 through 192 )A175 - 192
10X-RAY DIFFRACTION10chain 'A' and (resid 193 through 205 )A193 - 205
11X-RAY DIFFRACTION11chain 'A' and (resid 206 through 221 )A206 - 221
12X-RAY DIFFRACTION12chain 'B' and (resid 313 through 324 )B313 - 324

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