[English] 日本語
Yorodumi
- PDB-4jzc: Angiopoietin-2 fibrinogen domain TAG mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jzc
TitleAngiopoietin-2 fibrinogen domain TAG mutant
ComponentsAngiopoietin-2Angiopoietin
KeywordsSIGNALING PROTEIN / fibrinogen-like receptor-binding domain / Tie2 receptor-binding / Tie2
Function / homology
Function and homology information


negative regulation of positive chemotaxis / Tie signaling pathway / glomerulus vasculature development / negative regulation of cell-substrate adhesion / germ cell development / negative regulation of blood vessel endothelial cell migration / maternal process involved in female pregnancy / animal organ regeneration / response to glucose / response to mechanical stimulus ...negative regulation of positive chemotaxis / Tie signaling pathway / glomerulus vasculature development / negative regulation of cell-substrate adhesion / germ cell development / negative regulation of blood vessel endothelial cell migration / maternal process involved in female pregnancy / animal organ regeneration / response to glucose / response to mechanical stimulus / Tie2 Signaling / negative regulation of angiogenesis / response to activity / cell projection / response to organic cyclic compound / receptor tyrosine kinase binding / cellular response to growth factor stimulus / positive regulation of angiogenesis / gene expression / angiogenesis / collagen-containing extracellular matrix / response to hypoxia / signaling receptor binding / signal transduction / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain ...Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYu, X. / Seegar, T.C.M. / Dalton, A.C. / Tzvetkova-Robev, D. / Goldgur, Y. / Nikolov, D.B. / Barton, W.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis for angiopoietin-1-mediated signaling initiation.
Authors: Yu, X. / Seegar, T.C. / Dalton, A.C. / Tzvetkova-Robev, D. / Goldgur, Y. / Rajashankar, K.R. / Nikolov, D.B. / Barton, W.A.
History
DepositionApr 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Angiopoietin-2


Theoretical massNumber of molelcules
Total (without water)24,8181
Polymers24,8181
Non-polymers00
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Angiopoietin-2

A: Angiopoietin-2


Theoretical massNumber of molelcules
Total (without water)49,6352
Polymers49,6352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area1220 Å2
ΔGint-10 kcal/mol
Surface area17700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.692, 79.055, 135.544
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Angiopoietin-2 / Angiopoietin / ANG-2


Mass: 24817.604 Da / Num. of mol.: 1 / Fragment: fibrinogen-like receptor-binding domain / Mutation: P183T, Q184A, R185G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANGPT2 / Plasmid: modified pcDNA3.1 hygro / Cell line (production host): HEK293 / Production host: homo sapiens (human) / References: UniProt: O15123
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.0 M Na/K-tartate, 0.1 M Tris, 0.2 M LiSO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 4, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 29840 / Num. obs: 27572 / % possible obs: 92.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellHighest resolution: 1.6 Å / % possible all: 92.4

-
Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ang-2 fibrinogen-like domain

Resolution: 1.9→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 962 -random
Rwork0.23 ---
all-20239 --
obs-19930 98.5 %-
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 0 0 189 1937

+
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