[English] 日本語
Yorodumi
- PDB-8z73: Crystal Structure of AF9 in complex with H3K9la peptide -

+
Open data


ID or keywords:

Loading...

-
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 / 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 ...modification-dependent protein binding / 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 / : / negative regulation of canonical Wnt signaling pathway / euchromatin / structural constituent of chromatin / nucleosome / chromosome / positive regulation of cell growth / gene expression / molecular adaptor activity / histone binding / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more