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- PDB-4nft: Crystal structure of human lnkH2B-h2A.Z-Anp32e -

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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 / postsynaptic endosome membrane / histone chaperone activity / Swr1 complex / nucleosomal DNA binding / heterochromatin / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine ...phosphatase inhibitor activity / postsynaptic endosome membrane / histone chaperone activity / Swr1 complex / nucleosomal DNA binding / heterochromatin / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / Meiotic synapsis / protein folding chaperone / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / innate immune response in mucosa / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / cellular response to estradiol stimulus / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / euchromatin / postsynaptic density membrane / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Meiotic recombination / chromatin DNA binding / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / synaptic vesicle membrane / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / antibacterial humoral response / nucleosome / heterochromatin formation / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / cytoplasmic vesicle / Oxidative Stress Induced Senescence / regulation of apoptotic process / Estrogen-dependent gene expression / histone binding / defense response to Gram-positive bacterium / Ub-specific processing proteases / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Acidic leucine-rich nuclear phosphoprotein 32 / Leucine-rich repeat / Histone, subunit A / Histone, subunit A / Leucine-rich repeat profile. / : / Histone H2B signature. / Histone H2B / Histone H2B / Leucine-rich repeat ...Acidic leucine-rich nuclear phosphoprotein 32 / Leucine-rich repeat / Histone, subunit A / Histone, subunit A / Leucine-rich repeat profile. / : / Histone H2B signature. / Histone H2B / Histone H2B / Leucine-rich repeat / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Leucine-rich repeat domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / 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
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
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

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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


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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