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- PDB-7zud: Crystal structure of HIV-1 capsid IP6-CPSF6 complex -

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Basic information

Entry
Database: PDB / ID: 7zud
TitleCrystal structure of HIV-1 capsid IP6-CPSF6 complex
Components
  • Capsid protein p24
  • Cleavage and polyadenylation specificity factor subunit 6
KeywordsVIRAL PROTEIN / Complex / cofactor / host-factor
Function / homology
Function and homology information


exon-exon junction complex binding / : / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / interchromatin granule / Processing of Intronless Pre-mRNAs / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / paraspeckles ...exon-exon junction complex binding / : / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / interchromatin granule / Processing of Intronless Pre-mRNAs / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / paraspeckles / mRNA 3'-end processing / mRNA 3'-end processing / Signaling by cytosolic FGFR1 fusion mutants / RNA Polymerase II Transcription Termination / protein heterotetramerization / ribosomal large subunit binding / Processing of Capped Intron-Containing Pre-mRNA / localization / Signaling by FGFR1 in disease / protein tetramerization / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / mRNA processing / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / nuclear speck / ribonucleoprotein complex / symbiont entry into host cell / mRNA binding / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / cytoplasm
Similarity search - Function
Cleavage and polyadenylation specificity factor subunit 6 / CPSF6/7 family / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Reverse transcriptase connection / Reverse transcriptase connection domain / RNA-binding domain superfamily / Reverse transcriptase thumb ...Cleavage and polyadenylation specificity factor subunit 6 / CPSF6/7 family / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Reverse transcriptase connection / Reverse transcriptase connection domain / RNA-binding domain superfamily / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Gag-Pol 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 / Resolution: 2.93 Å
AuthorsNicastro, G. / Taylor, I.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
The Francis Crick InstituteFC001178 United Kingdom
Wellcome Trust108014/Z/15/Z United Kingdom
Citation
Journal: J.Mol.Biol. / Year: 2022
Title: CP-MAS and Solution NMR Studies of Allosteric Communication in CA-assemblies of HIV-1.
Authors: Nicastro, G. / Lucci, M. / Oregioni, A. / Kelly, G. / Frenkiel, T.A. / Taylor, I.A.
#1: Journal: Cell / Year: 2009
Title: X-ray structures of the hexameric building block of the HIV capsid.
Authors: Pornillos, O. / Ganser-Pornillos, B.K. / Kelly, B.N. / Hua, Y. / Whitby, F.G. / Stout, C.D. / Sundquist, W.I. / Hill, C.P. / Yeager, M.
#2: Journal: Proc Natl Acad Sci U S A / Year: 2014
Title: Structural basis of HIV-1 capsid recognition by PF74 and CPSF6.
Authors: Bhattacharya, A. / Alam, S.L. / Fricke, T. / Zadrozny, K. / Sedzicki, J. / Taylor, A.B. / Demeler, B. / Pornillos, O. / Ganser-Pornillos, B.K. / Diaz-Griffero, F. / Ivanov, D.N. / Yeager, M.
#3: Journal: 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.
#4: Journal: Nature / Year: 2018
Title: Inositol phosphates are assembly co-factors for HIV-1.
Authors: Dick, R.A. / Zadrozny, K.K. / Xu, C. / Schur, F.K.M. / Lyddon, T.D. / Ricana, C.L. / Wagner, J.M. / Perilla, J.R. / Ganser-Pornillos, B.K. / Johnson, M.C. / Pornillos, O. / Vogt, V.M.
History
DepositionMay 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein p24
M: Cleavage and polyadenylation specificity factor subunit 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4044
Polymers27,0842
Non-polymers1,3202
Water1086
1
A: Capsid protein p24
M: Cleavage and polyadenylation specificity factor subunit 6
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)170,42524
Polymers162,50512
Non-polymers7,92012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_775-x+2,-y+2,z1
crystal symmetry operation5_565y,-x+y+1,z1
crystal symmetry operation6_655x-y+1,x,z1
Buried area30610 Å2
ΔGint-352 kcal/mol
Surface area59410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.741, 90.741, 56.588
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Space group name HallP6
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-501-

IHP

21A-501-

IHP

31A-502-

IHP

41A-604-

HOH

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Components

#1: Protein Capsid protein p24 / CA


Mass: 25703.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: isolate NY5 / Gene: gag-pol / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12497
#2: Protein/peptide Cleavage and polyadenylation specificity factor subunit 6 / Cleavage and polyadenylation specificity factor 68 kDa subunit / CPSF 68 kDa subunit / Cleavage ...Cleavage and polyadenylation specificity factor 68 kDa subunit / CPSF 68 kDa subunit / Cleavage factor Im complex 68 kDa subunit / CFIm68 / Pre-mRNA cleavage factor Im 68 kDa subunit / Protein HPBRII-4/7


Mass: 1380.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16630
#3: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.3M Calcium chloride dihydrate, 0.3 M Magnesium chloride hexahydrate, 0.1 M Tris hydrochloride pH 8.5, 0.1 M Bicine, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9688 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9688 Å / Relative weight: 1
ReflectionResolution: 2.93→78.58 Å / Num. obs: 5698 / % possible obs: 98.4 % / Redundancy: 1 % / Biso Wilson estimate: 61.42 Å2 / CC1/2: 0.984 / Net I/σ(I): 7.6
Reflection shellResolution: 2.93→3.23 Å / Num. unique obs: 1717 / CC1/2: 0.425

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata processing
STARANISOdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3h47

3h47


Resolution: 2.93→78.58 Å / SU ML: 0.5208 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 39.819
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.336 511 8.97 %
Rwork0.2783 5187 -
obs0.2777 5698 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.9 Å2
Refinement stepCycle: LAST / Resolution: 2.93→78.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 72 6 1764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00461886
X-RAY DIFFRACTIONf_angle_d0.73992615
X-RAY DIFFRACTIONf_chiral_restr0.0919288
X-RAY DIFFRACTIONf_plane_restr0.0091314
X-RAY DIFFRACTIONf_dihedral_angle_d35.6444357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.93-3.030.37261000.32681239X-RAY DIFFRACTION92.86
3.03-3.230.32761530.28151324X-RAY DIFFRACTION99.46
3.23-3.690.36451300.26541295X-RAY DIFFRACTION99.86
3.7-4.660.33781280.26371329X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: 67.231075919 Å / Origin y: 88.3320904565 Å / Origin z: 11.0531490963 Å
111213212223313233
T0.194956933336 Å2-0.0359375316912 Å2-0.0446850291528 Å2-0.161863658763 Å2-0.0179216965141 Å2--0.459804951612 Å2
L0.745601760073 °2-0.555695840349 °20.80209377925 °2-0.707966931802 °2-1.18928771962 °2--1.83094518051 °2
S0.0778888726388 Å °-0.247960135006 Å °-0.00782812774307 Å °-0.200168814669 Å °-0.0882211650479 Å °-0.0573380079 Å °-0.0420770899002 Å °0.184916574786 Å °0.0469898876795 Å °
Refinement TLS groupSelection details: all

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