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- PDB-8z73: Crystal Structure of AF9 in complex with H3K9la peptide -

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Basic information

Entry
Database: PDB / ID: 8z73
TitleCrystal Structure of AF9 in complex with H3K9la peptide
Components
  • Histone H3.3C
  • Protein AF-9
KeywordsPEPTIDE BINDING PROTEIN / YEATS domain
Function / homology
Function and homology information


modification-dependent protein binding / histone H3K9ac reader activity / histone H3K18ac reader activity / histone H3K27ac reader activity / regulation of stem cell division / segment specification / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / anterior/posterior pattern specification / nucleosomal DNA binding ...modification-dependent protein binding / histone H3K9ac reader activity / histone H3K18ac reader activity / histone H3K27ac reader activity / regulation of stem cell division / segment specification / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / anterior/posterior pattern specification / nucleosomal DNA binding / hematopoietic stem cell differentiation / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / : / RNA Polymerase II Pre-transcription Events / transcription elongation factor complex / euchromatin / negative regulation of canonical Wnt signaling pathway / structural constituent of chromatin / nucleosome / chromosome / positive regulation of cell growth / histone binding / gene expression / molecular adaptor activity / protein heterodimerization activity / chromatin binding / positive regulation of DNA-templated transcription / DNA binding / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
AF-9, ANC1 homology domain / : / ANC1 homology domain (AHD) / : / YEATS superfamily / YEATS family / YEATS domain profile. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 ...AF-9, ANC1 homology domain / : / ANC1 homology domain (AHD) / : / YEATS superfamily / YEATS family / YEATS domain profile. / 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
Similarity search - Domain/homology
Protein AF-9 / Histone H3.3C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.906 Å
AuthorsLi, H.T. / Ma, H.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To be published
Title: Crystal Structure of AF9 in complex with H3K9la peptide
Authors: Ma, H.D. / Li, H.T.
History
DepositionApr 19, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein AF-9
P: Histone H3.3C
B: Protein AF-9
C: Histone H3.3C
D: Protein AF-9
E: Histone H3.3C
F: Protein AF-9
G: Histone H3.3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,13512
Polymers78,8878
Non-polymers2484
Water1,982110
1
A: Protein AF-9
P: Histone H3.3C


Theoretical massNumber of molelcules
Total (without water)19,7222
Polymers19,7222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein AF-9
C: Histone H3.3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7843
Polymers19,7222
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Protein AF-9
E: Histone H3.3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7843
Polymers19,7222
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Protein AF-9
G: Histone H3.3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8464
Polymers19,7222
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.587, 116.587, 168.824
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Protein AF-9 / ALL1-fused gene from chromosome 9 protein / Myeloid/lymphoid or mixed-lineage leukemia translocated ...ALL1-fused gene from chromosome 9 protein / Myeloid/lymphoid or mixed-lineage leukemia translocated to chromosome 3 protein / YEATS domain-containing protein 3


Mass: 18500.256 Da / Num. of mol.: 4 / Fragment: N-terminally processed
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT3, AF9, YEATS3 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42568
#2: Protein/peptide
Histone H3.3C / Histone H3.5


Mass: 1221.387 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6NXT2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 4.2 Å3/Da / Density % sol: 73.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 2.4M Sodium Malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 29694 / % possible obs: 99.5 % / Redundancy: 6.8 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.043 / Rrim(I) all: 0.115 / Χ2: 1.005 / Net I/σ(I): 7.9 / Num. measured all: 202935
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.9-2.956.80.78314560.8910.9710.3240.850.471100
2.95-36.60.70614790.9270.9810.2970.7680.50199.9
3-3.066.20.54514760.9340.9830.2390.5970.501100
3.06-3.126.50.4814620.9530.9880.2040.5230.543100
3.12-3.1970.37214540.9650.9910.1510.4020.59100
3.19-3.276.90.31114660.9770.9940.1270.3370.633100
3.27-3.356.50.26214880.980.9950.1110.2850.69399.9
3.35-3.446.70.20614630.9860.9960.0860.2240.778100
3.44-3.547.40.17714890.990.9970.0710.1910.9299.9
3.54-3.657.30.14514760.9940.9990.0580.1571.00199.9
3.65-3.787.30.13314600.9920.9980.0530.1431.11399.9
3.78-3.947.20.10714940.9940.9980.0430.1161.14199.9
3.94-4.117.20.09714770.9940.9990.0390.1051.28299.6
4.11-4.337.20.07914700.9970.9990.0320.0861.37899.1
4.33-4.670.0714870.9950.9990.0290.0761.53699.1
4.6-4.966.90.06114870.9970.9990.0250.0671.51699.2
4.96-5.466.40.0615000.9970.9990.0250.0651.35999.7
5.46-6.246.30.05815140.9980.9990.0250.0631.20699.7
6.24-7.866.60.0515400.9980.9990.0210.0541.20299.4
7.86-506.80.04415560.99810.0170.0471.53395.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3247: ???)refinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TMP

4tmp


Resolution: 2.906→24.964 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2205 1427 4.83 %
Rwork0.1956 --
obs0.1968 29561 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.906→24.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4877 0 16 110 5003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015029
X-RAY DIFFRACTIONf_angle_d1.1276766
X-RAY DIFFRACTIONf_dihedral_angle_d26.9561926
X-RAY DIFFRACTIONf_chiral_restr0.066698
X-RAY DIFFRACTIONf_plane_restr0.007879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.906-30.33881280.29122743X-RAY DIFFRACTION98
3.0093-3.12960.28491480.25842797X-RAY DIFFRACTION100
3.1296-3.27170.24491460.2432762X-RAY DIFFRACTION100
3.2717-3.44380.2461420.22322820X-RAY DIFFRACTION100
3.4438-3.65890.25031320.2042816X-RAY DIFFRACTION100
3.6589-3.94040.20781500.19572796X-RAY DIFFRACTION100
3.9404-4.33510.2051380.17922808X-RAY DIFFRACTION99
4.3351-4.95810.17421260.14992842X-RAY DIFFRACTION99
4.9581-6.23060.19291500.17472857X-RAY DIFFRACTION100
6.23-24.960.21691670.19282893X-RAY DIFFRACTION97

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