[English] 日本語
Yorodumi
- PDB-8bv1: Peptide inhibitor P4 in complex with ASF1 histone chaperone -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bv1
TitlePeptide inhibitor P4 in complex with ASF1 histone chaperone
Components
  • Histone chaperone ASF1A
  • P4 peptide inhibitor of histone chaperone ASF1
KeywordsCHAPERONE / Inhibitor / ASF1 / Histone / protein-protein interaction
Function / homology
Function and homology information


histone chaperone activity / DNA replication-dependent chromatin assembly / muscle cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA repair-dependent chromatin remodeling / replication fork processing / osteoblast differentiation / nucleosome assembly / site of double-strand break / histone binding ...histone chaperone activity / DNA replication-dependent chromatin assembly / muscle cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA repair-dependent chromatin remodeling / replication fork processing / osteoblast differentiation / nucleosome assembly / site of double-strand break / histone binding / DNA repair / chromatin binding / chromatin / protein-containing complex / nucleoplasm / nucleus
Similarity search - Function
Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone
Similarity search - Domain/homology
Histone chaperone ASF1A
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.834 Å
AuthorsPerrin, M.E. / Li, B. / Mbianda, J. / Ropars, V. / Legrand, P. / Douat, C. / Ochsenbein, F. / Guichard, G.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE18-0038 France
Fondation ARCPGA1*20160203953 France
Agence Nationale de la Recherche (ANR)ANR-20-CE18-0038 France
CitationJournal: Chem.Commun.(Camb.) / Year: 2023
Title: Unexpected binding modes of inhibitors to the histone chaperone ASF1 revealed by a foldamer scanning approach.
Authors: Perrin, M.E. / Li, B. / Mbianda, J. / Bakail, M. / Andre, C. / Moal, G. / Legrand, P. / Ropars, V. / Douat, C. / Ochsenbein, F. / Guichard, G.
History
DepositionDec 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.accession_code

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone chaperone ASF1A
B: Histone chaperone ASF1A
C: Histone chaperone ASF1A
D: Histone chaperone ASF1A
E: Histone chaperone ASF1A
F: Histone chaperone ASF1A
N: P4 peptide inhibitor of histone chaperone ASF1
G: P4 peptide inhibitor of histone chaperone ASF1
K: P4 peptide inhibitor of histone chaperone ASF1
H: P4 peptide inhibitor of histone chaperone ASF1
L: P4 peptide inhibitor of histone chaperone ASF1
I: P4 peptide inhibitor of histone chaperone ASF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,40227
Polymers116,02012
Non-polymers1,38115
Water2,648147
1
A: Histone chaperone ASF1A
N: P4 peptide inhibitor of histone chaperone ASF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8898
Polymers19,3372
Non-polymers5536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-13 kcal/mol
Surface area8700 Å2
MethodPISA
2
B: Histone chaperone ASF1A
K: P4 peptide inhibitor of histone chaperone ASF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6135
Polymers19,3372
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-6 kcal/mol
Surface area8720 Å2
MethodPISA
3
C: Histone chaperone ASF1A
I: P4 peptide inhibitor of histone chaperone ASF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4293
Polymers19,3372
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-5 kcal/mol
Surface area8370 Å2
MethodPISA
4
D: Histone chaperone ASF1A
L: P4 peptide inhibitor of histone chaperone ASF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4293
Polymers19,3372
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-4 kcal/mol
Surface area8600 Å2
MethodPISA
5
E: Histone chaperone ASF1A
G: P4 peptide inhibitor of histone chaperone ASF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6135
Polymers19,3372
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-6 kcal/mol
Surface area8730 Å2
MethodPISA
6
F: Histone chaperone ASF1A
H: P4 peptide inhibitor of histone chaperone ASF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4293
Polymers19,3372
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-6 kcal/mol
Surface area8600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.885, 123.885, 179.308
Angle α, β, γ (deg.)90, 90, 90
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein
Histone chaperone ASF1A / Anti-silencing function protein 1 homolog A / hAsf1a / CCG1-interacting factor A / hCIA


Mass: 17927.998 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Histone chaperone that facilitates histone deposition and histone exchange and removal during nucleosome assembly and disassembly
Source: (gene. exp.) Homo sapiens (human) / Gene: ASF1A, CGI-98, HSPC146 / Plasmid: pETM30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q9Y294
#2: Protein/peptide
P4 peptide inhibitor of histone chaperone ASF1


Mass: 1408.718 Da / Num. of mol.: 6 / Source method: obtained synthetically
Details: Sequence of a short alpha-helical peptide known to bind ASF1
Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5 30% (w/v) PEG 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2022 / Details: KB Mirrors
RadiationMonochromator: 0.97857 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.834→49.372 Å / Num. obs: 56883 / % possible obs: 88.79 % / Redundancy: 14.27 % / CC1/2: 0.9979 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.043 / Rrim(I) all: 0.162 / Net I/σ(I): 13.13
Reflection shellResolution: 2.834→2.907 Å / Redundancy: 13.97 % / Mean I/σ(I) obs: 1.446 / Num. unique obs: 1058 / CC1/2: 0.6066 / Rpim(I) all: 0.635 / % possible all: 22.49

-
Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
STARANISOdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6f0h

6f0h


Resolution: 2.834→29.79 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.942 / SU R Cruickshank DPI: 0.355 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.332 / SU Rfree Blow DPI: 0.239 / SU Rfree Cruickshank DPI: 0.248
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 2830 4.98 %RANDOM
Rwork0.2037 ---
obs0.2045 56834 88.8 %-
Displacement parametersBiso mean: 99.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.0137 Å20 Å20 Å2
2--0.0137 Å20 Å2
3----0.0273 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.834→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8045 0 90 147 8282
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088324HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9111335HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2850SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1511HARMONIC5
X-RAY DIFFRACTIONt_it8324HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1038SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5456SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion19.6
LS refinement shellResolution: 2.834→2.91 Å
RfactorNum. reflection% reflection
Rfree0.3283 53 -
Rwork0.3207 1084 -
obs--23.15 %
Refinement TLS params.

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)
15.8652-0.9998-2.89390.96280.63514.9189-0.0105-0.20920.0331-0.2092-0.053-0.14030.0331-0.14030.0634-0.2097-0.04320.0444-0.15380.0326-0.113-57.111634.2595-17.5294
22.77790.53930.94825.36751.44734.6809-0.0889-0.4488-0.332-0.44880.13810.2567-0.3320.2567-0.0492-0.09130.010.1768-0.25790.0482-0.09-21.347826.1306-40.295
33.3401-0.4125-1.17426.1384-1.26615.5977-0.26061.01440.37811.01440.10750.19350.37810.19350.15320.3464-0.00150.197-0.22640.098-0.0394-37.257166.4618-33.5468
44.59020.72570.20716.8837-0.19353.8933-0.0419-0.94160.622-0.94160.0537-0.52270.622-0.5227-0.01180.3169-0.0994-0.0894-0.1742-0.0279-0.1243-44.78424.6957-57.5592
56.4920.19162.24042.77270.82524.95130.2113-0.03940.5504-0.0394-0.0873-0.70490.5504-0.7049-0.124-0.2271-0.0484-0.00010.3172-0.0272-0.0396-16.176120.2012-6.255
66.65730.1285-0.27164.56381.75914.11380.140.0807-0.57970.08070.11250.7825-0.57970.7825-0.2526-0.1858-0.11990.04460.4981-0.3040.1798-15.448446.71015.1477
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|* N|*}A1 - 155
2X-RAY DIFFRACTION1{A|* N|*}N0
3X-RAY DIFFRACTION1{A|* N|*}N1 - 2
4X-RAY DIFFRACTION1{A|* N|*}N3
5X-RAY DIFFRACTION1{A|* N|*}N4 - 10
6X-RAY DIFFRACTION1{A|* N|*}N11
7X-RAY DIFFRACTION2{B|* K|*}B2 - 156
8X-RAY DIFFRACTION2{B|* K|*}K0
9X-RAY DIFFRACTION2{B|* K|*}K1 - 2
10X-RAY DIFFRACTION2{B|* K|*}K3
11X-RAY DIFFRACTION2{B|* K|*}K4 - 10
12X-RAY DIFFRACTION2{B|* K|*}K11
13X-RAY DIFFRACTION3{C|* I|*}C2 - 153
14X-RAY DIFFRACTION3{C|* I|*}I0
15X-RAY DIFFRACTION3{C|* I|*}I1 - 2
16X-RAY DIFFRACTION3{C|* I|*}I3
17X-RAY DIFFRACTION3{C|* I|*}I4 - 10
18X-RAY DIFFRACTION3{C|* I|*}I11
19X-RAY DIFFRACTION4{D|* L|*}D2 - 155
20X-RAY DIFFRACTION4{D|* L|*}L0
21X-RAY DIFFRACTION4{D|* L|*}L1 - 2
22X-RAY DIFFRACTION4{D|* L|*}L3
23X-RAY DIFFRACTION4{D|* L|*}L4 - 10
24X-RAY DIFFRACTION4{D|* L|*}L11
25X-RAY DIFFRACTION5{E|* G|*}E2 - 155
26X-RAY DIFFRACTION5{E|* G|*}G0
27X-RAY DIFFRACTION5{E|* G|*}G1 - 2
28X-RAY DIFFRACTION5{E|* G|*}G3
29X-RAY DIFFRACTION5{E|* G|*}G4 - 10
30X-RAY DIFFRACTION5{E|* G|*}G11
31X-RAY DIFFRACTION6{F|* H|*}F2 - 155
32X-RAY DIFFRACTION6{F|* H|*}H0
33X-RAY DIFFRACTION6{F|* H|*}H1 - 2
34X-RAY DIFFRACTION6{F|* H|*}H3
35X-RAY DIFFRACTION6{F|* H|*}H4 - 10
36X-RAY DIFFRACTION6{F|* H|*}H11

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more