[English] 日本語
Yorodumi
- PDB-6m3h: Crystal structure of mouse HPF1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6m3h
TitleCrystal structure of mouse HPF1
ComponentsHistone PARylation factor 1
KeywordsNUCLEAR PROTEIN / cofactor / ADP-ribosylation / DNA damage response
Function / homology
Function and homology information


protein ADP-ribosyltransferase-substrate adaptor activity / poly-ADP-D-ribose binding / DNA repair-dependent chromatin remodeling / site of DNA damage / double-strand break repair / histone binding / DNA damage response / chromatin binding / chromatin / nucleus
Similarity search - Function
Histone PARylation factor 1 / Histone PARylation factor 1
Similarity search - Domain/homology
Histone PARylation factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsSun, F.H. / Yun, C.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31270769 China
CitationJournal: Nat Commun / Year: 2021
Title: HPF1 remodels the active site of PARP1 to enable the serine ADP-ribosylation of histones.
Authors: Sun, F.H. / Zhao, P. / Zhang, N. / Kong, L.L. / Wong, C.C.L. / Yun, C.H.
History
DepositionMar 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone PARylation factor 1


Theoretical massNumber of molelcules
Total (without water)39,3521
Polymers39,3521
Non-polymers00
Water4,936274
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.031, 79.895, 106.674
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Histone PARylation factor 1


Mass: 39352.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hpf1
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q8CFE2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 300 K / Method: vapor diffusion
Details: 0.1M Tris-pH8.3, 0.2 M Potassium citrate tribasic monohydrate, 20% w/v PEG 3350,

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97849 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Dec 7, 2018
RadiationMonochromator: Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97849 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. obs: 39364 / % possible obs: 99.3 % / Redundancy: 5.7 % / Biso Wilson estimate: 21.62 Å2 / Rpim(I) all: 0.023 / Net I/σ(I): 31.1
Reflection shellResolution: 1.71→1.77 Å / Num. unique obs: 2485 / Rpim(I) all: 0.351

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M3G

6m3g


Resolution: 1.71→44.36 Å / SU ML: 0.1648 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 21.0794 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2175 1925 4.89 %
Rwork0.1821 37439 -
obs0.1838 39364 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.28 Å2
Refinement stepCycle: LAST / Resolution: 1.71→44.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2477 0 0 274 2751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652548
X-RAY DIFFRACTIONf_angle_d0.94313443
X-RAY DIFFRACTIONf_chiral_restr0.0636375
X-RAY DIFFRACTIONf_plane_restr0.0049447
X-RAY DIFFRACTIONf_dihedral_angle_d19.4903960
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.750.3221060.26892485X-RAY DIFFRACTION92.3
1.75-1.80.28081340.22962578X-RAY DIFFRACTION97.94
1.8-1.850.22171390.20462651X-RAY DIFFRACTION99.64
1.85-1.910.22221380.19352673X-RAY DIFFRACTION99.54
1.91-1.980.24421250.19052627X-RAY DIFFRACTION99.78
1.98-2.060.18551320.18342656X-RAY DIFFRACTION99.75
2.06-2.150.22811450.18272676X-RAY DIFFRACTION100
2.15-2.270.20971370.18352663X-RAY DIFFRACTION99.96
2.27-2.410.2151410.18492683X-RAY DIFFRACTION100
2.41-2.60.22121400.18572692X-RAY DIFFRACTION100
2.6-2.860.22651520.19042695X-RAY DIFFRACTION100
2.86-3.270.21441440.18542720X-RAY DIFFRACTION100
3.27-4.120.19591510.16212745X-RAY DIFFRACTION100
4.12-44.360.21981410.17162895X-RAY DIFFRACTION99.77

+
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