[English] 日本語
Yorodumi
- PDB-5bt1: histone chaperone Hif1 playing with histone H2A-H2B dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bt1
Titlehistone chaperone Hif1 playing with histone H2A-H2B dimer
Components
  • HAT1-interacting factor 1
  • Histone H2A.1
  • Histone H2B.1
KeywordsCHAPERONE / Histone chaperone complex / TPR / NASP homolog / assembly
Function / homology
Function and homology information


HATs acetylate histones / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / replication fork protection complex / Oxidative Stress Induced Senescence / RMTs methylate histone arginines ...HATs acetylate histones / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / replication fork protection complex / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / postreplication repair / RNA Polymerase I Promoter Escape / Estrogen-dependent gene expression / histone acetyltransferase complex / subtelomeric heterochromatin formation / Ub-specific processing proteases / nucleosomal DNA binding / heterochromatin formation / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / histone binding / chromosome, telomeric region / protein heterodimerization activity / DNA repair / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / nucleus
Similarity search - Function
Histone, subunit A / Histone, subunit A / Tetratricopeptide repeat domain / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A ...Histone, subunit A / Histone, subunit A / Tetratricopeptide repeat domain / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H2B.1 / Histone H2A.1 / HAT1-interacting factor 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.62 Å
AuthorsLiu, H. / Zhang, M. / Gao, Y. / Teng, M. / Niu, L.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2012CB917200 China
Ministry of Science and Technology (China)2011CBA00800 China
Chinese National Natural Science Foundation31130018 China
Chinese National Natural Science Foundation31170726 China
CitationJournal: Structure / Year: 2016
Title: Structural Insights into the Association of Hif1 with Histones H2A-H2B Dimer and H3-H4 Tetramer
Authors: Zhang, M. / Liu, H. / Gao, Y. / Zhu, Z. / Chen, Z. / Zheng, P. / Xue, L. / Li, J. / Teng, M. / Niu, L.
History
DepositionJun 2, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 8, 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: HAT1-interacting factor 1
B: HAT1-interacting factor 1
C: Histone H2A.1
D: Histone H2B.1


Theoretical massNumber of molelcules
Total (without water)119,9994
Polymers119,9994
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8430 Å2
ΔGint-47 kcal/mol
Surface area32090 Å2
Unit cell
Length a, b, c (Å)102.673, 48.363, 160.706
Angle α, β, γ (deg.)90.000, 107.050, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein HAT1-interacting factor 1


Mass: 44553.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HIF1, YLL022C, L1205 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12373
#2: Protein Histone H2A.1


Mass: 15312.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HTA1, H2A1, SPT11, YDR225W, YD9934.10 / Production host: Escherichia coli (E. coli) / References: UniProt: P04911
#3: Protein Histone H2B.1 / Suppressor of Ty protein 12


Mass: 15579.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HTB1, H2B1, SPT12, YDR224C, YD9934.09C / Production host: Escherichia coli (E. coli) / References: UniProt: P02293
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 1.59 Å3/Da / Density % sol: 22.61 % / Description: Rod-shaped crystals
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / Details: 0.1M Magnesium formate dihydrate, 15% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.62→50 Å / Num. obs: 22738 / % possible obs: 98.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.062 / Rrim(I) all: 0.123 / Χ2: 1.83 / Net I/av σ(I): 13.773 / Net I/σ(I): 7.4 / Num. measured all: 80873
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.62-2.673.50.62611250.6830.3750.7341.32498.7
2.67-2.713.50.56711160.7330.3410.6661.23597.3
2.71-2.773.50.53211120.7780.3160.6221.27399.5
2.77-2.823.50.46811730.7740.2810.5491.22299
2.82-2.883.50.40411040.8270.240.4731.29198.8
2.88-2.953.50.36111160.8610.2150.4231.25399.2
2.95-3.023.50.311460.9040.1790.3511.25598.5
3.02-3.113.50.28311410.8960.170.3321.42199.6
3.11-3.23.50.22311210.940.1320.2611.41598.7
3.2-3.33.50.211410.9520.1190.2341.56398.7
3.3-3.423.50.16411420.970.0960.1911.61899
3.42-3.563.60.13611440.9730.0810.1591.72899.3
3.56-3.723.60.12611460.9710.0740.1472.48699.2
3.72-3.913.50.09411200.9850.0560.112.08398.9
3.91-4.163.60.07611280.990.0450.0891.6898.5
4.16-4.483.60.06311470.9930.0370.0741.86897.9
4.48-4.933.60.05411290.9950.0310.0621.44597.3
4.93-5.643.80.06311590.9940.0360.0731.38798.1
5.64-7.113.70.05511540.9960.0310.0631.37797.5
7.11-503.60.03311740.9980.0190.0387.30195.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NQ0

4nq0


Resolution: 2.62→43.38 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.898 / SU B: 27.95 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.644 / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2618 1162 5.1 %RANDOM
Rwork0.2075 ---
obs0.2104 21504 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 95.17 Å2 / Biso mean: 45.253 Å2 / Biso min: 22.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å21.66 Å2
2---0.32 Å20 Å2
3---0.8 Å2
Refinement stepCycle: final / Resolution: 2.62→43.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5270 0 0 47 5317
Biso mean---45.45 -
Num. residues----668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225350
X-RAY DIFFRACTIONr_angle_refined_deg1.0491.977222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6815662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.21324.771262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.08815974
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2871537
X-RAY DIFFRACTIONr_chiral_restr0.0690.2821
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214017
X-RAY DIFFRACTIONr_mcbond_it0.5331.53330
X-RAY DIFFRACTIONr_mcangle_it1.00725323
X-RAY DIFFRACTIONr_scbond_it1.22532020
X-RAY DIFFRACTIONr_scangle_it2.1744.51899
LS refinement shellResolution: 2.62→2.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 79 -
Rwork0.282 1591 -
all-1670 -
obs--97.04 %
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)
10.43810.83050.15761.82890.4070.40540.0596-0.077-0.0051-0.0494-0.1173-0.040.01050.02480.05770.12080.00350.02810.10120.00180.1156-12.6734-4.1717-63.4318
20.34970.098-0.11981.7246-1.13390.7952-0.0109-0.00660.01380.0464-0.01160.0688-0.02010.02940.02250.1218-0.03840.00980.0956-0.01090.1259-42.6583-1.5173-19.1718
32.0705-0.2615-0.7163.0256-1.59271.3583-0.124-0.1231-0.28010.04310.02620.1666-0.10580.13360.09780.1171-0.0541-0.03520.14720.1030.1116-16.71695.8583-35.5902
41.78650.2751-0.24112.8296-2.28942.0138-0.1616-0.1248-0.15960.0655-0.0801-0.1094-0.08850.18610.24170.0498-0.0455-0.00220.12770.08340.1504-15.02099.8439-38.126
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 346
2X-RAY DIFFRACTION2B17 - 345
3X-RAY DIFFRACTION3C16 - 100
4X-RAY DIFFRACTION4D37 - 126

+
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