[English] 日本語
Yorodumi
- PDB-1ae5: HUMAN HEPARIN BINDING PROTEIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ae5
TitleHUMAN HEPARIN BINDING PROTEIN
ComponentsHEPARIN BINDING PROTEIN
KeywordsSERINE PROTEASE HOMOLOG / ENDOTOXIN BINDING / HEPARIN BINDING / INFLAMMATION / ANTIBACTERIAL / CAP37 / AZUROCIDIN / GLYCOSYLATED PROTEIN
Function / homology
Function and homology information


monocyte extravasation / neutrophil-mediated killing of bacterium / monocyte activation / cellular extravasation / positive regulation of fractalkine production / glial cell migration / induction of positive chemotaxis / regulation of vascular permeability / antimicrobial humoral response / positive regulation of MHC class II biosynthetic process ...monocyte extravasation / neutrophil-mediated killing of bacterium / monocyte activation / cellular extravasation / positive regulation of fractalkine production / glial cell migration / induction of positive chemotaxis / regulation of vascular permeability / antimicrobial humoral response / positive regulation of MHC class II biosynthetic process / heparan sulfate proteoglycan binding / azurophil granule / azurophil granule membrane / macrophage chemotaxis / toxic substance binding / positive regulation of cell adhesion / positive regulation of phagocytosis / protein maturation / positive regulation of interleukin-1 beta production / cell chemotaxis / microglial cell activation / positive regulation of tumor necrosis factor production / azurophil granule lumen / peptidase activity / heparin binding / defense response to Gram-negative bacterium / phospholipase C-activating G protein-coupled receptor signaling pathway / defense response to virus / intracellular signal transduction / inflammatory response / serine-type endopeptidase activity / intracellular membrane-bounded organelle / Neutrophil degranulation / negative regulation of apoptotic process / proteolysis / extracellular space / extracellular exosome / extracellular region / membrane
Similarity search - Function
Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsIversen, L.F. / Kastrup, J.S. / Bjorn, S.E. / Rasmussen, P.B. / Wiberg, F.C. / Flodgaard, H.J. / Larsen, I.K.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Structure of HBP, a multifunctional protein with a serine proteinase fold.
Authors: Iversen, L.F. / Kastrup, J.S. / Bjorn, S.E. / Rasmussen, P.B. / Wiberg, F.C. / Flodgaard, H.J. / Larsen, I.K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallization and Molecular Replacement Solution of Human Heparin Binding Protein
Authors: Iversen, L.F. / Kastrup, J.S. / Larsen, I.K. / Bjorn, S.E. / Rasmussen, P.B. / Wiberg, F.C. / Flodgaard, H.J.
#2: Journal: FEBS Lett. / Year: 1996
Title: Characterization of Recombinant Human Hbp/CAP37/Azurocidin, a Pleiotropic Mediator of Inflammation-Enhancing Lps-Induced Cytokine Release from Monocytes
Authors: Rasmussen, P.B. / Bjorn, S. / Hastrup, S. / Nielsen, P.F. / Norris, K. / Thim, L. / Wiberg, F.C. / Flodgaard, H.
History
DepositionMar 5, 1997Processing site: BNL
Revision 1.0Mar 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 2, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HEPARIN BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7453
Polymers24,3021
Non-polymers4422
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.190, 66.120, 101.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein HEPARIN BINDING PROTEIN / CAP37 / AZUROCIDIN


Mass: 24302.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: SF-900 / Cell line (production host): SF-900 / Production host: unidentified baculovirus / Strain (production host): ACMNPV / References: UniProt: P20160
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 7.2 / Details: pH 7.2
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Iversen, L.F., (1996) Acta Crystallogr.,Sect.D, 52, 1222.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 mg/mlprotein1drop
27-10 %ethanol1drop
32.5-5 %glycerol1drop
40.05 MTris-HCl1drop
514-20 %ethanol1reservoir
65-10 %glycerol1reservoir
70.1 MTris-HCl1reservoir

-
Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.999
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 12176 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 14.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.264 / % possible all: 98.6
Reflection shell
*PLUS
% possible obs: 98.6 %

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
TNTrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PPF

1ppf


Resolution: 2.3→20 Å / σ(F): 1
Details: THERE IS A DISORDERED REGION IN THE STRUCTURE INVOLVING RESIDUES 44 - 48.
Num. reflection% reflection
all12176 -
obs12176 99.2 %
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 28 63 1778
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.4
X-RAY DIFFRACTIONt_dihedral_angle_d18.43
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it2.6
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.192 / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.43

+
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