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- PDB-4u0a: Hexameric HIV-1 CA in complex with CPSF6 peptide, P6 crystal form -

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Basic information

Entry
Database: PDB / ID: 4u0a
TitleHexameric HIV-1 CA in complex with CPSF6 peptide, P6 crystal form
Components
  • Capsid protein p24
  • Cleavage and polyadenylation specificity factor subunit 6
KeywordsVIRAL PROTEIN / Capsid
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 / host multivesicular body / ISG15 antiviral mechanism / 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 / 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
Gag polyprotein / Cleavage and polyadenylation specificity factor subunit 6
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsPrice, A.J. / Jacques, D.A. / James, L.C.
CitationJournal: Plos Pathog. / Year: 2014
Title: Host Cofactors and Pharmacologic Ligands Share an Essential Interface in HIV-1 Capsid That Is Lost upon Disassembly.
Authors: Price, A.J. / Jacques, D.A. / McEwan, W.A. / Fletcher, A.J. / Essig, S. / Chin, J.W. / Halambage, U.D. / Aiken, C. / James, L.C.
History
DepositionJul 11, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 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 / diffrn_radiation_wavelength / 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.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Nov 13, 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: Capsid protein p24
B: Cleavage and polyadenylation specificity factor subunit 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0483
Polymers27,0122
Non-polymers351
Water2,648147
1
A: Capsid protein p24
B: Cleavage and polyadenylation specificity factor subunit 6
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)162,28518
Polymers162,07212
Non-polymers2136
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 area23290 Å2
ΔGint-252 kcal/mol
Surface area60570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.549, 91.549, 57.001
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-452-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein Capsid protein p24 / Pr55Gag


Mass: 25461.271 Da / Num. of mol.: 1 / Mutation: A14C,E45C,W184A,M185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B
Strain: isolate NY5 / Gene: gag / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12493
#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: 1550.796 Da / Num. of mol.: 1 / Fragment: UNP residues 313-327 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16630
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.6M sodium potassium tartrate tetrahydrate, 0.1M TRIS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.05→79.284 Å / Num. all: 17251 / Num. obs: 17251 / % possible obs: 100 % / Redundancy: 7.3 % / Rsym value: 0.266 / Net I/σ(I): 4.6
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.05-2.166.80.9730.31715025280.4190.9732100
2.16-2.296.70.9460.41572623560.4030.9462.2100
2.29-2.457.60.4071.51689622190.1570.4073.6100
2.45-2.657.30.3571.81515020750.1410.3574.2100
2.65-2.97.30.3770.71384319020.1530.377599.9
2.9-3.247.90.212.81369517280.0790.216.5100
3.24-3.747.20.2321.71117015430.0930.2326.7100
3.74-4.587.60.1791.3991013030.070.1797.5100
4.58-6.487.40.1085.6751410180.0420.1087.6100
6.48-46.28170.0884.840275790.0380.0887.799.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.68 Å46.28 Å
Translation5.68 Å46.28 Å

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
REFMAC5.8.0073refinement
iMOSFLMdata reduction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3H47

3h47


Resolution: 2.05→79.28 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2656 / WRfactor Rwork: 0.2259 / FOM work R set: 0.8054 / SU B: 10.218 / SU ML: 0.141 / SU R Cruickshank DPI: 0.2041 / SU Rfree: 0.1785 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2525 864 5.1 %RANDOM
Rwork0.2128 16208 --
obs0.2147 17072 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.22 Å2 / Biso mean: 27.74 Å2 / Biso min: 12.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å2-0 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 2.05→79.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1698 0 1 147 1846
Biso mean--20.53 32.44 -
Num. residues----222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0191742
X-RAY DIFFRACTIONr_bond_other_d0.0010.021659
X-RAY DIFFRACTIONr_angle_refined_deg0.831.9642370
X-RAY DIFFRACTIONr_angle_other_deg0.7073.0013826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3515220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3272572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.18115285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.262159
X-RAY DIFFRACTIONr_chiral_restr0.0470.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211959
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02370
X-RAY DIFFRACTIONr_mcbond_it1.6192.67886
X-RAY DIFFRACTIONr_mcbond_other1.6192.667885
X-RAY DIFFRACTIONr_mcangle_it2.6474.4671101
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 45 -
Rwork0.314 1135 -
all-1180 -
obs--92.69 %
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)
10.39650.33280.04830.90950.37390.46210.00620.00940.0423-0.0685-0.04940.0053-0.0363-0.07310.04320.02710.0176-0.00510.04420.01050.0385-20.702216.73660.6844
25.9413-1.14143.12591.3139-2.06577.79320.2396-0.1121-0.3434-0.0068-0.13970.23010.3408-0.4323-0.09990.0283-0.04870.01020.1143-0.0530.0741-35.27370.6623-1.9446
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 220
2X-RAY DIFFRACTION2B313 - 326

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