[English] 日本語
Yorodumi
- PDB-8j69: Crystal structure of HORMA domain-containing protein 1 (HORMAD1) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8j69
TitleCrystal structure of HORMA domain-containing protein 1 (HORMAD1) from Homo sapiens
ComponentsHORMA domain-containing protein 1
KeywordsPROTEIN BINDING / HORMA domain-containing protein 1 / adaptor
Function / homology
Function and homology information


regulation of homologous chromosome segregation / meiotic DNA double-strand break formation / meiotic recombination checkpoint signaling / synaptonemal complex assembly / meiotic sister chromatid cohesion / synaptonemal complex / oogenesis / blastocyst development / meiotic cell cycle / chromosome ...regulation of homologous chromosome segregation / meiotic DNA double-strand break formation / meiotic recombination checkpoint signaling / synaptonemal complex assembly / meiotic sister chromatid cohesion / synaptonemal complex / oogenesis / blastocyst development / meiotic cell cycle / chromosome / spermatogenesis / nucleus
Similarity search - Function
HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily
Similarity search - Domain/homology
HORMA domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsYang, X.Y. / Liu, X.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Structure / Year: 2023
Title: Structural and biochemical insights into the interaction mechanism underlying HORMAD1 and its partner proteins.
Authors: Wang, H. / Xie, R. / Niu, F. / Yang, Q. / An, L. / Wu, C. / Liu, X. / Yang, X.
History
DepositionApr 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HORMA domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)45,2591
Polymers45,2591
Non-polymers00
Water543
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)53.367, 64.498, 81.643
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein HORMA domain-containing protein 1


Mass: 45259.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HORMAD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86X24
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 1.55 Å3/Da / Density % sol: 20.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 4% TacsimateTM PH6.0, 12% (w/v) Polyethylene

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.67→50.61 Å / Num. obs: 15433 / % possible obs: 99.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.1
Reflection shellResolution: 2.67→2.74 Å / Redundancy: 6.4 % / Num. unique obs: 3844 / CC1/2: 0.972

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→50.61 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 1470 9.53 %
Rwork0.2036 --
obs0.2084 15433 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.67→50.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 0 3 1815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081853
X-RAY DIFFRACTIONf_angle_d1.0132508
X-RAY DIFFRACTIONf_dihedral_angle_d5.578244
X-RAY DIFFRACTIONf_chiral_restr0.058282
X-RAY DIFFRACTIONf_plane_restr0.007317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.770.35051470.27211390X-RAY DIFFRACTION100
2.77-2.880.30431550.2521406X-RAY DIFFRACTION100
2.88-3.010.34081590.26411363X-RAY DIFFRACTION100
3.01-3.170.31211420.24561431X-RAY DIFFRACTION100
3.17-3.360.2661550.21051393X-RAY DIFFRACTION100
3.36-3.620.23981230.22051410X-RAY DIFFRACTION100
3.62-3.990.2851480.21081389X-RAY DIFFRACTION100
3.99-4.570.25621530.17221380X-RAY DIFFRACTION100
4.57-5.750.20861290.17851424X-RAY DIFFRACTION100
5.76-50.610.21591590.19571377X-RAY DIFFRACTION99

+
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