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- PDB-4cay: Crystal structure of a human Anp32e-H2A.Z-H2B complex -

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Basic information

Entry
Database: PDB / ID: 4cay
TitleCrystal structure of a human Anp32e-H2A.Z-H2B complex
Components
  • ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER E
  • HISTONE H2A.Z
  • HISTONE H2B TYPE 1-J
KeywordsTRANSCRIPTION / EPIGENETICS / NUCLEOSOME / HISTONE VARIANT / HISTONE CHAPERONE
Function / homology
Function and homology information


phosphatase inhibitor activity / postsynaptic endosome membrane / histone chaperone activity / Swr1 complex / negative regulation of tumor necrosis factor-mediated signaling pathway / RNA polymerase II core promoter sequence-specific DNA binding / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / heterochromatin / CENP-A containing nucleosome ...phosphatase inhibitor activity / postsynaptic endosome membrane / histone chaperone activity / Swr1 complex / negative regulation of tumor necrosis factor-mediated signaling pathway / RNA polymerase II core promoter sequence-specific DNA binding / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / heterochromatin / CENP-A containing nucleosome / protein folding chaperone / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / ChAHP complex assembly / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / FXIIa activates plasma kallikrein-kinin system / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Meiotic synapsis / DNA methylation / Condensation of Prophase Chromosomes / cellular response to estradiol stimulus / 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 / NuRD complex assembly / Regulation of endogenous retroelements by KRAB-ZFP proteins / Interaction of NuRD complexes with transcription factors / Defective pyroptosis / HDACs deacetylate histones / CHD1 and CHD2 subfamily / Transcriptional regulation by small RNAs / lipopolysaccharide binding / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / euchromatin / CHD6, CHD7, CHD8, CHD9 subfamily / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / chromatin DNA binding / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / Formation of the beta-catenin:TCF transactivating complex / postsynaptic density membrane / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / nucleosomal DNA binding / innate immune response in mucosa / synaptic vesicle membrane / histone binding / structural constituent of chromatin / nucleosome assembly / Regulation of PD-L1(CD274) transcription / nucleosome / HATs acetylate histones / E3 ubiquitin ligases ubiquitinate target proteins / killing of cells of another organism / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Processing of DNA double-strand break ends / Dengue Virus-Host Interactions / antimicrobial humoral immune response mediated by antimicrobial peptide / Senescence-Associated Secretory Phenotype (SASP) / cytoplasmic vesicle / heterochromatin formation / defense response to Gram-negative bacterium / Oxidative Stress Induced Senescence / antibacterial humoral response / Estrogen-dependent gene expression / regulation of apoptotic process / 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 exosome / nucleoplasm / extracellular region / nucleus
Similarity search - Function
Acidic leucine-rich nuclear phosphoprotein 32 / Leucine-rich repeat / Histone, subunit A / Histone, subunit A / Leucine-rich repeat profile. / Leucine-rich repeat / : / : / Leucine-rich repeat domain superfamily / Histone H2A conserved site ...Acidic leucine-rich nuclear phosphoprotein 32 / Leucine-rich repeat / Histone, subunit A / Histone, subunit A / Leucine-rich repeat profile. / Leucine-rich repeat / : / : / Leucine-rich repeat domain superfamily / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H2B type 1-J / Histone H2A.Z / Acidic leucine-rich nuclear phosphoprotein 32 family member E
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsObri, A. / Ouararhni, K. / Papin, C. / Diebold, M.-L. / Padmanabhan, K. / Marek, M. / Stoll, I. / Roy, L. / Reilly, P.T. / Mak, T.W. ...Obri, A. / Ouararhni, K. / Papin, C. / Diebold, M.-L. / Padmanabhan, K. / Marek, M. / Stoll, I. / Roy, L. / Reilly, P.T. / Mak, T.W. / Dimitrov, S. / Romier, C. / Hamiche, A.
CitationJournal: Nature / Year: 2014
Title: Anp32E is a Histone Chaperone that Removes H2A.Z from Chromatin
Authors: Obri, A. / Ouararhni, K. / Papin, C. / Diebold, M.-L. / Padmanabhan, K. / Marek, M. / Stoll, I. / Roy, L. / Reilly, P.T. / Wak, T.W. / Dimitrov, S. / Romier, C. / Hamiche, A.
History
DepositionOct 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Structure summary
Revision 1.3Mar 9, 2016Group: Structure summary
Revision 1.4Dec 14, 2016Group: Structure summary
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HISTONE H2A.Z
B: HISTONE H2B TYPE 1-J
C: ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER E


Theoretical massNumber of molelcules
Total (without water)26,3963
Polymers26,3963
Non-polymers00
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-54.1 kcal/mol
Surface area10060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.816, 66.076, 45.293
Angle α, β, γ (deg.)90.00, 95.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HISTONE H2A.Z / H2A/Z


Mass: 12020.978 Da / Num. of mol.: 1 / Fragment: GLOBULAR DOMAIN, RESIDUES 19-128
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNCS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0C0S5
#2: Protein HISTONE H2B TYPE 1-J / HISTONE H2B.1 / HISTONE H2B.R / H2B/R / H2B


Mass: 10881.576 Da / Num. of mol.: 1 / Fragment: GLOBULAR DOMAIN, RESIDUES 31-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNCS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06899
#3: Protein/peptide ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER E / LANP-LIKE PROTEIN / LANP-L / ANP32E


Mass: 3493.605 Da / Num. of mol.: 1 / Fragment: H2A.Z INTERACTING DOMAIN (ZID), RESIDUES 215-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNEA-TH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BTT0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE METHIONINE AT THE START OF THE MACROMOLECULAR SEQUENCE (CHAIN A) IS AN EXPRESSION ARTEFACT THE ...THE METHIONINE AT THE START OF THE MACROMOLECULAR SEQUENCE (CHAIN A) IS AN EXPRESSION ARTEFACT THE METHIONINE AT THE START OF THE MACROMOLECULAR SEQUENCE (CHAIN B) IS AN EXPRESSION ARTEFACT THE GLY-SER AND HIS-MET RESIDUES AT THE BEGINNING OF THE MACROMOLECULAR SEQUENCE (CHAIN C) ARE ARTEFACTS FROM THE THROMBIN CLEAVAGE SITE AND THE CLONING SITE, RESPECTIVELY

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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: 1.84 Å3/Da / Density % sol: 33 % / Description: NONE
Crystal growDetails: 0.1 M NA CACODYLATE, PH 7.0, 0.2 M NA FORMATE, 24% TO 30% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 30963 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 16.54 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 39.7
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 5.5 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F66

1f66


Resolution: 1.48→37.23 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.9516 / SU R Cruickshank DPI: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.072 / SU Rfree Blow DPI: 0.072 / SU Rfree Cruickshank DPI: 0.071
RfactorNum. reflection% reflectionSelection details
Rfree0.1952 1537 4.99 %RANDOM
Rwork0.168 ---
obs0.1694 30793 98.93 %-
Displacement parametersBiso mean: 23.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.1317 Å20 Å20.486 Å2
2--1.9784 Å20 Å2
3----1.8467 Å2
Refine analyzeLuzzati coordinate error obs: 0.189 Å
Refinement stepCycle: LAST / Resolution: 1.48→37.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1563 0 0 212 1775
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011647HARMONIC2
X-RAY DIFFRACTIONt_angle_deg12229HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d626SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes38HARMONIC2
X-RAY DIFFRACTIONt_gen_planes253HARMONIC5
X-RAY DIFFRACTIONt_it1647HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion15.06
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion226SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2271SEMIHARMONIC4
LS refinement shellResolution: 1.48→1.53 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.1952 138 4.59 %
Rwork0.1829 2868 -
all0.1835 3006 -
obs--98.93 %
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)
10.35360.48480.06213.01550.14760.9026-0.09550.05410.0069-0.32660.11010.048-0.08450.0026-0.0146-0.0235-0.0090.0114-0.03030.0004-0.04115.1879-0.525313.5588
20.34520.6275-0.00582.4209-0.43690.6533-0.06290.0558-0.0507-0.15840.0529-0.0054-0.0242-0.01670.0101-0.04120.00480.0135-0.0368-0.0004-0.019515.4976-7.201716.6244
30.2389-2.0409-1.20142.4873-1.28940.3798-0.04460.09070.1489-0.43190.0291-0.4501-0.14570.38590.01550.1067-0.15250.0058-0.01970.0531-0.128423.34519.86922.9333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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