[English] 日本語
Yorodumi
- PDB-8e08: Crystal structure of HPSE P6 in complex with tetraose pentosan in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 800000000
TitleCrystal structure of HPSE P6 in complex with tetraose pentosan inhibitor
Components
  • Heparanase 50 kDa subunit
  • Heparanase 8 kDa subunit
KeywordsHYDROLASE / Heparanase / Heparan Sulfate
Function / homology
Function and homology information


heparanase / heparanase activity / regulation of hair follicle development / heparin proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / HS-GAG degradation / positive regulation of hair follicle development / syndecan binding / proteoglycan metabolic process ...heparanase / heparanase activity / regulation of hair follicle development / heparin proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / HS-GAG degradation / positive regulation of hair follicle development / syndecan binding / proteoglycan metabolic process / vascular wound healing / protein transmembrane transport / establishment of endothelial barrier / angiogenesis involved in wound healing / positive regulation of osteoblast proliferation / positive regulation of vascular endothelial growth factor production / positive regulation of blood coagulation / extracellular matrix / lysosomal lumen / cell-matrix adhesion / specific granule lumen / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / membrane raft / lysosomal membrane / response to antibiotic / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular space / extracellular region / nucleoplasm / nucleus
Similarity search - Function
Glycoside hydrolase, family 79 / Glycosyl hydrolase family 79, N-terminal domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Heparanase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsWhitefield, C. / Jackson, C.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)LP160101552 Australia
CitationJournal: Biochemistry / Year: 2023
Title: Complex Inhibitory Mechanism of Glycomimetics with Heparanase.
Authors: Whitefield, C. / Vo, Y. / Schwartz, B.D. / Hepburn, C. / Ahmed, F.H. / Onagi, H. / Banwell, M.G. / Nelms, K. / Malins, L.R. / Jackson, C.J.
History
DepositionAug 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 2.0Nov 13, 2024Group: Atomic model / Data collection / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heparanase 50 kDa subunit
B: Heparanase 8 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7559
Polymers53,6432
Non-polymers4,1117
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11500 Å2
ΔGint-263 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.274, 75.627, 125.467
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Heparanase 50 kDa subunit


Mass: 43375.863 Da / Num. of mol.: 1
Mutation: N178K, A195S, L197G, S212A, S219D, L230R, D234G, E244K, Q248H, R273G, S292A, R307L, I318T, S322Q, F327L, L354G, S426Q, K427D, K477Q, L483H, H486D, L498Q, M512K, E513P, S530A, A540P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9Y251
#2: Protein Heparanase 8 kDa subunit


Mass: 10267.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9Y251

-
Sugars , 1 types, 3 molecules

#3: Polysaccharide 2,3,4-tri-O-sulfo-beta-D-xylopyranose-(1-4)-2,3-di-O-sulfo-beta-D-xylopyranose-(1-4)-2,3-di-O-sulfo- ...2,3,4-tri-O-sulfo-beta-D-xylopyranose-(1-4)-2,3-di-O-sulfo-beta-D-xylopyranose-(1-4)-2,3-di-O-sulfo-beta-D-xylopyranose-(1-4)-2,3-di-O-sulfo-beta-D-xylopyranose


Type: oligosaccharide / Mass: 1267.042 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
[][b-D-Xylp2SO33SO3]{[(4+1)][b-D-Xylp2SO33SO3]{[(4+1)][b-D-Xylp2SO33SO3]{[(4+1)][b-D-Xylp2SO33SO34SO3]{}}}}LINUCSPDB-CARE

-
Non-polymers , 3 types, 314 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M Ammonium Sulfate, Sodium Acetate pH 5.5, 20% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.93→48.28 Å / Num. obs: 43216 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.033 / Rrim(I) all: 0.12 / Χ2: 0.75 / Net I/σ(I): 11.8 / Num. measured all: 561577
Reflection shellResolution: 1.93→1.98 Å / % possible obs: 100 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.925 / Num. measured all: 38828 / Num. unique obs: 2843 / CC1/2: 0.938 / Rpim(I) all: 0.257 / Rrim(I) all: 0.96 / Χ2: 0.39 / Net I/σ(I) obs: 3

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RG8

7rg8


Resolution: 1.93→48.28 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2018 2111 4.9 %
Rwork0.1727 --
obs0.1741 43065 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3628 0 237 310 4175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073968
X-RAY DIFFRACTIONf_angle_d1.1125433
X-RAY DIFFRACTIONf_dihedral_angle_d13.8371398
X-RAY DIFFRACTIONf_chiral_restr0.057604
X-RAY DIFFRACTIONf_plane_restr0.006649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.970.32341340.25022677X-RAY DIFFRACTION100
1.97-2.020.28421350.21052679X-RAY DIFFRACTION100
2.02-2.080.23861350.19652707X-RAY DIFFRACTION100
2.08-2.140.19481330.18032704X-RAY DIFFRACTION100
2.14-2.210.20861360.1742703X-RAY DIFFRACTION100
2.21-2.290.2961270.21852666X-RAY DIFFRACTION97
2.29-2.380.25481430.1852687X-RAY DIFFRACTION100
2.38-2.490.24871420.18162715X-RAY DIFFRACTION100
2.49-2.620.19031730.17612699X-RAY DIFFRACTION100
2.62-2.780.20651480.17352698X-RAY DIFFRACTION100
2.78-30.20311380.17692755X-RAY DIFFRACTION100
3-3.30.19471400.17682756X-RAY DIFFRACTION100
3.3-3.780.2041420.15552771X-RAY DIFFRACTION100
3.78-4.760.1371260.14262808X-RAY DIFFRACTION100
4.76-48.280.19591590.17712929X-RAY DIFFRACTION100

+
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