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- PDB-5fug: Crystal structure of a human YL1-H2A.Z-H2B complex -

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Basic information

Entry
Database: PDB / ID: 5fug
TitleCrystal structure of a human YL1-H2A.Z-H2B complex
Components
  • HISTONE H2A.Z
  • HISTONE H2B TYPE 1-J
  • VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG
KeywordsDNA BINDING PROTEIN / HISTONE / CHAPERONE / REMODELER / H2A.Z / YL1
Function / homology
Function and homology information


ATP-dependent H2AZ histone chaperone activity / histone chaperone activity / regulation of double-strand break repair / NuA4 histone acetyltransferase complex / somatic stem cell population maintenance / positive regulation of double-strand break repair via homologous recombination / 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 / heterochromatin ...ATP-dependent H2AZ histone chaperone activity / histone chaperone activity / regulation of double-strand break repair / NuA4 histone acetyltransferase complex / somatic stem cell population maintenance / positive regulation of double-strand break repair via homologous recombination / 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 / heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / heterochromatin organization / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / transcription initiation-coupled chromatin remodeling / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / innate immune response in mucosa / Defective pyroptosis / cellular response to estradiol stimulus / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / euchromatin / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / DNA Damage/Telomere Stress Induced Senescence / chromatin DNA binding / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Processing of DNA double-strand break ends / histone binding / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / regulation of apoptotic process / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / Ub-specific processing proteases / regulation of cell cycle / defense response to Gram-positive bacterium / nuclear speck / chromatin remodeling / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Vps72/YL1, N-terminal / Vps72/YL1 family / YL1 nuclear protein / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain / Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B ...Vps72/YL1, N-terminal / Vps72/YL1 family / YL1 nuclear protein / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain / Histone, subunit A / Histone, subunit A / 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 / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H2B type 1-J / Histone H2A.Z / Vacuolar protein sorting-associated protein 72 homolog
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLatrick, C.M. / Marek, M. / Ouararhni, K. / Papin, C. / Stoll, I. / Ignatyeva, M. / Obri, A. / Ennifar, E. / Dimitrov, S. / Romier, C. / Hamiche, A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Molecular Basis and Specificity of H2A.Z-H2B Recognition and Deposition by the Histone Chaperone Yl1
Authors: Latrick, C.M. / Marek, M. / Ouararhni, K. / Papin, C. / Stoll, I. / Ignatyeva, M. / Obri, A. / Ennifar, E. / Dimitrov, S. / Romier, C. / Hamiche, A.
History
DepositionJan 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Mar 23, 2016Group: Database references
Revision 1.3Apr 20, 2016Group: Database references
Revision 1.4Jan 10, 2024Group: 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: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG
D: HISTONE H2A.Z
E: HISTONE H2B TYPE 1-J
F: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG
G: HISTONE H2A.Z
H: HISTONE H2B TYPE 1-J
I: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG
J: HISTONE H2A.Z
K: HISTONE H2B TYPE 1-J
L: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)120,74712
Polymers120,74712
Non-polymers00
Water1267
1
G: HISTONE H2A.Z
H: HISTONE H2B TYPE 1-J
I: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)30,1873
Polymers30,1873
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-54.5 kcal/mol
Surface area11830 Å2
MethodPISA
2
D: HISTONE H2A.Z
E: HISTONE H2B TYPE 1-J
F: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)30,1873
Polymers30,1873
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-51.8 kcal/mol
Surface area12570 Å2
MethodPISA
3
A: HISTONE H2A.Z
B: HISTONE H2B TYPE 1-J
C: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)30,1873
Polymers30,1873
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-53.7 kcal/mol
Surface area11880 Å2
MethodPISA
4
J: HISTONE H2A.Z
K: HISTONE H2B TYPE 1-J
L: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)30,1873
Polymers30,1873
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-46.3 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.120, 150.680, 92.610
Angle α, β, γ (deg.)90.00, 91.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11889.781 Da / Num. of mol.: 4 / Fragment: GLOBULAR DOMAIN
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 / HISTONE H2B


Mass: 10750.380 Da / Num. of mol.: 4 / Fragment: GLOBULAR DOMAIN
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: P06899
#3: Protein
VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG / PROTEIN YL-1 / TRANSCRIPTION FACTOR-LIKE 1 / HISTONE CHAPERON E YL1


Mass: 7546.579 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN
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: Q15906
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growDetails: 0.1 M SUCCINIC ACID/PHOSPHATE/GLYCINE SYSTEM PH 6/7 ; 25% PEG 1500

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 27631 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 64.74 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 14.1
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.97 / % possible all: 97.6

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Processing

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

1f66


Resolution: 2.7→44.25 Å / Cor.coef. Fo:Fc: 0.9463 / Cor.coef. Fo:Fc free: 0.9072 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.324
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 1677 6.22 %RANDOM
Rwork0.1774 ---
obs0.1816 26955 99.19 %-
Displacement parametersBiso mean: 56.11 Å2
Baniso -1Baniso -2Baniso -3
1--12.6446 Å20 Å2-4.2096 Å2
2--5.7706 Å20 Å2
3---6.8741 Å2
Refine analyzeLuzzati coordinate error obs: 0.393 Å
Refinement stepCycle: LAST / Resolution: 2.7→44.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7168 0 0 7 7175
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017261HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.189765HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2615SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes194HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1058HARMONIC5
X-RAY DIFFRACTIONt_it7261HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.37
X-RAY DIFFRACTIONt_other_torsion20.73
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion968SEMIHARMONIC5
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_contact8424SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.8 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3081 169 6.33 %
Rwork0.2168 2499 -
all0.2227 2668 -
obs--99.19 %
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)
11.95010.8129-1.58513.3165-2.30463.94370.0357-0.1281-0.03140.086-0.2109-0.1072-0.05770.25860.1752-0.06430.0219-0.0509-0.1664-0.0039-0.00483.414515.125616.135
24.10480.7077-1.92872.3468-3.18042.78580.0706-0.2071-0.0080.1885-0.06360.1966-0.14160.0097-0.007-0.1066-0.0305-0.0206-0.2064-0.005-0.0051-0.203714.982320.5141
30.2060.68630.01534.4688-2.34873.73970.03560.0917-0.02140.0855-0.0993-0.38380.01290.31390.0637-0.14050.03060.025-0.17530.0225-0.01629.073319.10611.96
41.6752-0.3770.652.92161.7283.994-0.0060.02470.1038-0.0842-0.08210.1304-0.2226-0.1280.08810.0635-0.00070.111-0.2377-0.0228-0.0558-4.7934-23.298510.4651
53.16520.05431.76572.02090.85351.6522-0.0281-0.18230.04520.07750.02170.03510.04420.05250.00640.11580.02550.0998-0.2339-0.0271-0.0936-2.0082-23.170916.757
61.27220.173-0.04042.75682.36232.9898-0.1240.00050.09750.2317-0.08490.3938-0.2085-0.12220.20890.05510.01190.0147-0.29680.0161-0.0753-9.8158-25.7138.2912
71.05630.09250.03452.1962-0.89863.25140.02710.0460.0004-0.1142-0.1377-0.04390.18680.14080.1107-0.02110.0326-0.0658-0.10030.0195-0.04956.595810.961-31.6104
83.25160.7148-1.11440.9239-2.12773.08640.05440.026-0.09790.14630.0251-0.03360.0839-0.0413-0.07960.00010.0026-0.0586-0.16720.0285-0.05843.463411.0611-25.4209
90.05660.63030.64242.7115-1.70513.2557-0.05150.0569-0.1750.2202-0.0539-0.41380.23010.39470.1054-0.09340.04140.0371-0.11480.0292-0.037712.23515.5133-34.3401
102.19231.6071.58843.18572.18043.99280.07170.03560.1177-0.1511-0.2173-0.0533-0.05560.01910.1456-0.02130.15110.0991-0.15810.0206-0.0435-1.2091-26.867-34.7262
113.01271.98891.9993.12172.35213.50030.1728-0.18540.03470.2331-0.1415-0.35790.00820.0333-0.0313-0.0280.11670.0609-0.192-0.0062-0.10281.6709-27.4298-29.8515
121.66370.2266-0.18253.20051.71663.4636-0.06460.16310.2248-0.0045-0.02070.268-0.2958-0.06030.0853-0.06230.1603-0.0209-0.22610.0689-0.132-7.7646-29.8053-38.3704
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN J
10X-RAY DIFFRACTION10CHAIN K
11X-RAY DIFFRACTION11CHAIN K
12X-RAY DIFFRACTION12CHAIN L

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