[English] 日本語
Yorodumi
- PDB-7hhh: PanDDA analysis group deposition -- Crystal structure of HRP-2 PW... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7hhh
TitlePanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1259335862
ComponentsHepatoma-derived growth factor-related protein 2
KeywordsGENE REGULATION / Inhibitor / Fragment screening / Epigenetic reader / methyllysine / PWWP / Diamond Light Source / I04-1 / PanDDA / XChem
Function / homology
Function and homology information


H3K27me3 modified histone binding / H3K9me3 modified histone binding / skeletal muscle tissue regeneration / muscle cell differentiation / muscle organ development / DNA repair-dependent chromatin remodeling / positive regulation of double-strand break repair via homologous recombination / methylated histone binding / histone reader activity / positive regulation of cell growth ...H3K27me3 modified histone binding / H3K9me3 modified histone binding / skeletal muscle tissue regeneration / muscle cell differentiation / muscle organ development / DNA repair-dependent chromatin remodeling / positive regulation of double-strand break repair via homologous recombination / methylated histone binding / histone reader activity / positive regulation of cell growth / DNA recombination / chromatin remodeling / DNA repair / nucleus / cytoplasm
Similarity search - Function
Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / TFIIS/LEDGF domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain
Similarity search - Domain/homology
: / Hepatoma-derived growth factor-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsVantieghem, T. / Osipov, E. / Fearon, D. / Douangamath, A. / von Delft, F. / Strelkov, S.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1SC9822N Belgium
Research Foundation - Flanders (FWO)1SC9824N Belgium
Research Foundation - Flanders (FWO)G053822N Belgium
CitationJournal: Eur.J.Med.Chem. / Year: 2024
Title: Rational fragment-based design of compounds targeting the PWWP domain of the HRP family.
Authors: Vantieghem, T. / Aslam, N.A. / Osipov, E.M. / Akele, M. / Van Belle, S. / Beelen, S. / Drexler, M. / Paulovcakova, T. / Lux, V. / Fearon, D. / Douangamath, A. / von Delft, F. / Christ, F. / ...Authors: Vantieghem, T. / Aslam, N.A. / Osipov, E.M. / Akele, M. / Van Belle, S. / Beelen, S. / Drexler, M. / Paulovcakova, T. / Lux, V. / Fearon, D. / Douangamath, A. / von Delft, F. / Christ, F. / Veverka, V. / Verwilst, P. / Van Aerschot, A. / Debyser, Z. / Strelkov, S.V.
History
DepositionAug 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hepatoma-derived growth factor-related protein 2
B: Hepatoma-derived growth factor-related protein 2
C: Hepatoma-derived growth factor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,97512
Polymers32,0953
Non-polymers8819
Water4,900272
1
A: Hepatoma-derived growth factor-related protein 2
hetero molecules


  • defined by author
  • 11 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)11,0485
Polymers10,6981
Non-polymers3504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hepatoma-derived growth factor-related protein 2
hetero molecules


  • defined by author
  • 11.1 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)11,0714
Polymers10,6981
Non-polymers3723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hepatoma-derived growth factor-related protein 2
hetero molecules


  • defined by author
  • 10.9 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)10,8563
Polymers10,6981
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.390, 41.960, 158.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Hepatoma-derived growth factor-related protein 2 / HDGF-related protein 2 / HRP-2 / Hepatoma-derived growth factor 2 / HDGF-2


Mass: 10698.171 Da / Num. of mol.: 3 / Mutation: C64S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDGFL2, HDGF2, HDGFRP2, HRP2, UNQ785/PRO1604 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z4V5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-A1A3T / 1-[(1-methyl-1H-pyrazol-4-yl)methyl]piperazine


Mass: 180.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 28% PEG MME 2000; 0.15 M ammonium sulfate; 0.1 M sodium acetate pH 4.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.918076 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: May 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918076 Å / Relative weight: 1
ReflectionResolution: 1.69→79.37 Å / Num. obs: 31927 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.039 / Rrim(I) all: 0.097 / Χ2: 0.99 / Net I/σ(I): 10.2 / Num. measured all: 198752
Reflection shellResolution: 1.69→1.73 Å / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 2.208 / Num. measured all: 14296 / Num. unique obs: 2331 / CC1/2: 0.332 / Rpim(I) all: 0.969 / Rrim(I) all: 2.415 / Χ2: 0.78 / Net I/σ(I) obs: 0.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
xia2data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→79.37 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.939 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25748 1672 5.2 %RANDOM
Rwork0.20446 ---
obs0.20728 30184 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.784 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2---0.08 Å20 Å2
3----0.91 Å2
Refinement stepCycle: 1 / Resolution: 1.69→79.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2149 0 51 272 2472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122304
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.8333134
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.275267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.18856
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11410307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1280.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021908
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5893.7371078
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.096.6741341
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.4274.0481226
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.856.013673
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.69→1.734 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 126 -
Rwork0.364 2198 -
obs--99.79 %

+
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