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- PDB-4b4n: CPSF6 defines a conserved capsid interface that modulates HIV-1 r... -

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Basic information

Entry
Database: PDB / ID: 4b4n
TitleCPSF6 defines a conserved capsid interface that modulates HIV-1 replication
Components
  • CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
  • GAG PROTEIN
KeywordsVIRAL PROTEIN/RNA BINDING PROTEIN / VIRAL PROTEIN-RNA BINDING PROTEIN COMPLEX / HIV-1 / CYCLOPHILIN
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 / ribosomal large subunit binding / Processing of Capped Intron-Containing Pre-mRNA / viral process / Signaling by FGFR1 in disease / protein tetramerization / mRNA processing / viral capsid / nuclear speck / ribonucleoprotein complex / mRNA binding / RNA binding / nucleoplasm / nucleus / membrane / cytoplasm
Similarity search - Function
Cleavage and polyadenylation specificity factor subunit 6 / CPSF6/7 family / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / : / gag protein p24 N-terminal domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...Cleavage and polyadenylation specificity factor subunit 6 / CPSF6/7 family / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / : / 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 / 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 / Retrovirus capsid, N-terminal / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Gag protein / Cleavage and polyadenylation specificity factor subunit 6
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.813 Å
AuthorsPrice, A.J. / James, L.C.
CitationJournal: Plos Pathog. / Year: 2012
Title: Cpsf6 Defines a Conserved Capsid Interface that Modulates HIV-1 Replication.
Authors: Price, A.J. / Fletcher, A.J. / Schaller, T. / Elliott, T. / Lee, K. / Kewalramani, V.N. / Chin, J.W. / Towers, G.J. / James, L.C.
History
DepositionJul 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GAG PROTEIN
B: CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6


Theoretical massNumber of molelcules
Total (without water)17,7552
Polymers17,7552
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-6.6 kcal/mol
Surface area8400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.560, 46.360, 80.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GAG PROTEIN


Mass: 16204.573 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 33-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: A9PKC6
#2: Protein/peptide CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6 / CPSF6 / CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 68 KDA SUBUNIT / CFIM68 / CPSF 68 KDA ...CPSF6 / CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 68 KDA SUBUNIT / CFIM68 / CPSF 68 KDA SUBUNIT / PRE-MRNA CLEAVAGE FACTOR IM 68 KDA SUBUNIT / PROTEIN HPBRII-4/7


Mass: 1550.796 Da / Num. of mol.: 1 / Fragment: RESIDUES 313-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q16630
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.52 % / Description: NONE
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 17 DEGREES (SITTING DROPS).PROTEIN/ PEPTIDE SOLUTION (0.37 MM HIV-1 CAN AND 4 MM CPSF6313-327 IN 20 MM HEPES PH 7, 50 MM NACL, 1 MM DTT) WAS MIXED WITH RESERVOIR SOLUTION (20% W/V PEG 3350, ...Details: 17 DEGREES (SITTING DROPS).PROTEIN/ PEPTIDE SOLUTION (0.37 MM HIV-1 CAN AND 4 MM CPSF6313-327 IN 20 MM HEPES PH 7, 50 MM NACL, 1 MM DTT) WAS MIXED WITH RESERVOIR SOLUTION (20% W/V PEG 3350, 0.2 M POTASSIUM PHOSPHATE DIBASIC) IN A 1:1 MIX.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 13664 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rsym value: 0.044 / Net I/σ(I): 14.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GON

2gon


Resolution: 1.813→36.251 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.918 / SU B: 8.731 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.334 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflection
Rfree0.2729 682 5.01 %
Rwork0.1867 --
obs0.191 13664 94.955 %
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 29.696 Å2
Baniso -1Baniso -2Baniso -3
1--0.196 Å20 Å20 Å2
2--0.08 Å20 Å2
3---0.116 Å2
Refinement stepCycle: LAST / Resolution: 1.813→36.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1178 0 0 99 1277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191217
X-RAY DIFFRACTIONr_bond_other_d0.0010.021179
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.9551656
X-RAY DIFFRACTIONr_angle_other_deg0.84732717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1965150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55424.71753
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14715203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.165157
X-RAY DIFFRACTIONr_chiral_restr0.0920.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211363
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02268
X-RAY DIFFRACTIONr_nbd_refined0.2580.2369
X-RAY DIFFRACTIONr_nbd_other0.2620.245
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2603
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.222
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_it17.1362.9141217
X-RAY DIFFRACTIONr_mcbond_other8.0932.9581179
X-RAY DIFFRACTIONr_mcangle_it19.954.3091655
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it26.8659.152147
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it22.96528.52959
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.46832396
X-RAY DIFFRACTIONr_sphericity_free29.738530
X-RAY DIFFRACTIONr_sphericity_bonded13.932434
LS refinement shellResolution: 1.813→1.86 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.494 53 -
Rwork0.314 861 -
obs--88.224 %

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