[English] 日本語
Yorodumi
- PDB-4nft: Crystal structure of human lnkH2B-h2A.Z-Anp32e -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nft
TitleCrystal structure of human lnkH2B-h2A.Z-Anp32e
Components
  • Acidic leucine-rich nuclear phosphoprotein 32 family member E
  • Histone H2B type 2-E, Histone H2A.Z
KeywordsCHAPERONE / Histone binding protein
Function / homology
Function and homology information


phosphatase inhibitor activity / Swr1 complex / histone exchange / nucleosomal DNA binding / Packaging Of Telomere Ends / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected purine / Deposition of new CENPA-containing nucleosomes at the centromere / heterochromatin / Inhibition of DNA recombination at telomere ...phosphatase inhibitor activity / Swr1 complex / histone exchange / nucleosomal DNA binding / Packaging Of Telomere Ends / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected purine / Deposition of new CENPA-containing nucleosomes at the centromere / heterochromatin / Inhibition of DNA recombination at telomere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA polymerase II core promoter sequence-specific DNA binding / Meiotic synapsis / heterochromatin assembly => GO:0031507 / RNA Polymerase I Promoter Opening / DNA methylation / HCMV Late Events / innate immune response in mucosa / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Condensation of Prophase Chromosomes / PRC2 methylates histones and DNA / euchromatin / RNA Polymerase I Promoter Escape / HDACs deacetylate histones / Transcriptional regulation by small RNAs / Nonhomologous End-Joining (NHEJ) / NoRC negatively regulates rRNA expression / cellular response to estradiol stimulus / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / B-WICH complex positively regulates rRNA expression / nucleosome assembly / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / RMTs methylate histone arginines / HCMV Early Events / chromatin DNA binding / Pre-NOTCH Transcription and Translation / Meiotic recombination / nucleosome / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / cytoplasmic vesicle / Oxidative Stress Induced Senescence / antibacterial humoral response / Estrogen-dependent gene expression / regulation of apoptotic process / antimicrobial humoral immune response mediated by antimicrobial peptide / Ub-specific processing proteases / defense response to Gram-positive bacterium / protein heterodimerization activity / Amyloid fiber formation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A signature. / Histone H2A conserved site / Leucine-rich repeat profile. / C-terminus of histone H2A / Histone H2A, C-terminal domain ...Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A signature. / Histone H2A conserved site / Leucine-rich repeat profile. / C-terminus of histone H2A / Histone H2A, C-terminal domain / Histone H2A / Histone 2A / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Core histone H2A/H2B/H3/H4 / Histone H2A/H2B/H3 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H2A.Z / Histone H2B type 2-E / Acidic leucine-rich nuclear phosphoprotein 32 family member E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsShan, S. / Pan, L. / Mao, Z. / Wang, W. / Sun, J. / Dong, Q. / Liang, X. / Ding, X. / Chen, S. / Dai, L. ...Shan, S. / Pan, L. / Mao, Z. / Wang, W. / Sun, J. / Dong, Q. / Liang, X. / Ding, X. / Chen, S. / Dai, L. / Zhang, Z. / Zhu, B. / Zhou, Z.
CitationJournal: Cell Res. / Year: 2014
Title: Anp32e, a higher eukaryotic histone chaperone directs preferential recognition for H2A.Z
Authors: Mao, Z. / Pan, L. / Wang, W. / Sun, J. / Shan, S. / Dong, Q. / Liang, X. / Dai, L. / Ding, X. / Chen, S. / Zhang, Z. / Zhu, B. / Zhou, Z.
History
DepositionNov 1, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone H2B type 2-E, Histone H2A.Z
B: Histone H2B type 2-E, Histone H2A.Z
C: Histone H2B type 2-E, Histone H2A.Z
D: Histone H2B type 2-E, Histone H2A.Z
E: Acidic leucine-rich nuclear phosphoprotein 32 family member E
F: Acidic leucine-rich nuclear phosphoprotein 32 family member E


Theoretical massNumber of molelcules
Total (without water)102,0916
Polymers102,0916
Non-polymers00
Water2,630146
1
A: Histone H2B type 2-E, Histone H2A.Z


Theoretical massNumber of molelcules
Total (without water)22,5091
Polymers22,5091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone H2B type 2-E, Histone H2A.Z


Theoretical massNumber of molelcules
Total (without water)22,5091
Polymers22,5091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Histone H2B type 2-E, Histone H2A.Z
F: Acidic leucine-rich nuclear phosphoprotein 32 family member E


Theoretical massNumber of molelcules
Total (without water)28,5372
Polymers28,5372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-10 kcal/mol
Surface area9810 Å2
MethodPISA
4
D: Histone H2B type 2-E, Histone H2A.Z
E: Acidic leucine-rich nuclear phosphoprotein 32 family member E


Theoretical massNumber of molelcules
Total (without water)28,5372
Polymers28,5372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-10 kcal/mol
Surface area9790 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)76.412, 104.297, 124.743
Angle α, β, γ (deg.)90.00, 99.15, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Histone H2B type 2-E, Histone H2A.Z / Histone H2B-GL105 / Histone H2B.q / H2B/q / H2A/z


Mass: 22508.875 Da / Num. of mol.: 4 / Fragment: UNP residues 34-126, 16-114
Source method: isolated from a genetically manipulated source
Details: Chimera of H2B and H2A.Z / Source: (gene. exp.) Homo sapiens (human) / Gene: H2BFQ, H2AZ / Production host: Escherichia coli (E. coli) / References: UniProt: Q16778, UniProt: P0C0S5
#2: Protein Acidic leucine-rich nuclear phosphoprotein 32 family member E / Anp32e / LANP-like protein / LANP-L


Mass: 6027.800 Da / Num. of mol.: 2 / Fragment: UNP residues 185-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANP32E / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BTT0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M Sodium thiocyanate, 20%(w/v) polyethylene glycol 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 29217 / % possible obs: 99.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 31.81 Å2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 99.9

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→39.795 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.5309 / SU ML: 0.2 / σ(F): 1.34 / Phase error: 46.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2727 1478 5.12 %RANDOM
Rwork0.2195 ---
obs0.2221 28845 98 %-
all-29217 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.73 Å2 / Biso mean: 31.3547 Å2 / Biso min: 12.17 Å2
Refinement stepCycle: LAST / Resolution: 2.61→39.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5772 0 0 146 5918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085866
X-RAY DIFFRACTIONf_angle_d1.0817888
X-RAY DIFFRACTIONf_chiral_restr0.071924
X-RAY DIFFRACTIONf_plane_restr0.005988
X-RAY DIFFRACTIONf_dihedral_angle_d17.6352212
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6104-2.69470.32221340.32394252895
2.6947-2.7910.37771260.285325112637100
2.791-2.90270.37251400.26872505264599
2.9027-3.03470.27941460.250225062652100
3.0347-3.19470.31231460.24832526267299
3.1947-3.39470.27641530.23122495264899
3.3947-3.65670.24471140.20882518263299
3.6567-4.02430.26971210.19892533265499
4.0243-4.60590.24131320.18042531266399
4.6059-5.80010.26711420.19772516265899
5.8001-39.79990.20061240.19042332245690

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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