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- PDB-7mju: Crystal structure of human AF10 PZP bound to histone H3 tail -

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Basic information

Entry
Database: PDB / ID: 7mju
TitleCrystal structure of human AF10 PZP bound to histone H3 tail
ComponentsHistone H3.1,Protein AF-10
KeywordsPEPTIDE BINDING PROTEIN / Histone binding Leukemia
Function / homology
Function and homology information


nucleosome binding / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes ...nucleosome binding / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Pre-NOTCH Transcription and Translation / Meiotic recombination / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RMTs methylate histone arginines / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / histone binding / gene expression / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane
Similarity search - Function
: / : / : / : / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. ...: / : / : / : / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Protein AF-10 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsKlein, B.J. / Kutateladze, T.G.
CitationJournal: Nat Commun / Year: 2021
Title: The role of the PZP domain of AF10 in acute leukemia driven by AF10 translocations.
Authors: Klein, B.J. / Deshpande, A. / Cox, K.L. / Xuan, F. / Zandian, M. / Barbosa, K. / Khanal, S. / Tong, Q. / Zhang, Y. / Zhang, P. / Sinha, A. / Bohlander, S.K. / Shi, X. / Wen, H. / Poirier, M. ...Authors: Klein, B.J. / Deshpande, A. / Cox, K.L. / Xuan, F. / Zandian, M. / Barbosa, K. / Khanal, S. / Tong, Q. / Zhang, Y. / Zhang, P. / Sinha, A. / Bohlander, S.K. / Shi, X. / Wen, H. / Poirier, M.G. / Deshpande, A.J. / Kutateladze, T.G.
History
DepositionApr 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3.1,Protein AF-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9376
Polymers22,6101
Non-polymers3275
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11010 Å2
Unit cell
Length a, b, c (Å)42.920, 54.330, 47.780
Angle α, β, γ (deg.)90.000, 106.820, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone H3.1,Protein AF-10


Mass: 22609.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, ...Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J, MLLT10, AF10
Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P68431, UniProt: P55197
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsamino-terminal thirteen residues of Histone H3.1 followed by SGS linker, and then the Histone H3- ...amino-terminal thirteen residues of Histone H3.1 followed by SGS linker, and then the Histone H3-interacting region of AF-10

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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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.09 M Tris, 22.5% PEG 3350, and 10 mM spermine tetrahydrochloride
PH range: 8.5-8.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.27819 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Aug 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27819 Å / Relative weight: 1
ReflectionResolution: 2.1→41.09 Å / Num. obs: 12143 / % possible obs: 97.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 28.17 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.9
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 845 / CC1/2: 0.637

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→41.084 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.79 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2059 631 5.21 %
Rwork0.1646 11491 -
obs0.1668 12122 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.34 Å2 / Biso mean: 35.5477 Å2 / Biso min: 11.13 Å2
Refinement stepCycle: final / Resolution: 2.1→41.084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1416 0 5 151 1572
Biso mean--25.78 42.61 -
Num. residues----184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071477
X-RAY DIFFRACTIONf_angle_d0.8281995
X-RAY DIFFRACTIONf_dihedral_angle_d7.8611175
X-RAY DIFFRACTIONf_chiral_restr0.051207
X-RAY DIFFRACTIONf_plane_restr0.005263
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1003-2.26250.2536970.1921211089
2.2625-2.49010.21311190.18522327100
2.4901-2.85040.24841560.18332307100
2.8504-3.59090.19861300.16112348100
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)
12.0609-0.0436-0.19462.40410.34432.16560.06110.1536-0.0218-0.1651-0.1439-0.03580.07070.05190.10550.15740.02350.00890.1693-0.01090.145922.6119.75963.7537
21.9756-0.3534-0.12952.62510.28311.69360.04760.039-0.0285-0.0489-0.12160.6096-0.0837-0.26270.07330.12760.0146-0.00810.1996-0.00910.18066.238515.843411.1417
31.96890.62360.23362.0521.3843.52290.1295-0.15950.16250.2456-0.05610.07090.0047-0.05610.02420.2527-0.00340.00930.15810.00330.192111.628126.6619.1219
42.43661.47780.99630.94610.7711.0725-0.13020.03960.4175-0.3197-0.1821-0.0656-0.14570.3280.13720.23070.0287-0.03390.27410.05310.274936.589214.28865.4067
55.34861.3252-0.69616.13471.54961.86070.06220.9092-0.1403-0.7042-0.20150.32410.3627-0.59690.16870.2207-0.0105-0.0610.2695-0.010.20355.445916.43763.7111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 79 )A23 - 79
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 148 )A92 - 148
3X-RAY DIFFRACTION3chain 'A' and (resid 149 through 203 )A149 - 203
4X-RAY DIFFRACTION4chain 'A' and (resid 1 through 12 )A1 - 12
5X-RAY DIFFRACTION5chain 'A' and (resid 80 through 85)A80 - 85

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