[English] 日本語
Yorodumi
- PDB-4epu: Ang1 fibrinogen-related domain (FReD) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4epu
TitleAng1 fibrinogen-related domain (FReD)
ComponentsAngiopoietin-1Angiopoietin
KeywordsSIGNALING PROTEIN / fibrinogen / signaling / Tie2/TEK / extracellular
Function / homology
Function and homology information


regulation of macrophage migration inhibitory factor signaling pathway / Tie signaling pathway / glomerulus vasculature development / positive regulation of blood-brain barrier permeability / heparin biosynthetic process / regulation of skeletal muscle satellite cell proliferation / negative regulation of cytokine production involved in immune response / regulation of tumor necrosis factor production / negative regulation of cell adhesion / protein localization to cell surface ...regulation of macrophage migration inhibitory factor signaling pathway / Tie signaling pathway / glomerulus vasculature development / positive regulation of blood-brain barrier permeability / heparin biosynthetic process / regulation of skeletal muscle satellite cell proliferation / negative regulation of cytokine production involved in immune response / regulation of tumor necrosis factor production / negative regulation of cell adhesion / protein localization to cell surface / negative regulation of vascular permeability / sprouting angiogenesis / regulation of canonical NF-kappaB signal transduction / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of protein import into nucleus / positive chemotaxis / cell-substrate adhesion / microvillus / positive regulation of receptor internalization / hemopoiesis / positive regulation of cell adhesion / positive regulation of blood vessel endothelial cell migration / negative regulation of endothelial cell apoptotic process / Tie2 Signaling / positive regulation of endothelial cell migration / negative regulation of protein phosphorylation / positive regulation of protein ubiquitination / receptor tyrosine kinase binding / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of peptidyl-serine phosphorylation / RAF/MAP kinase cascade / collagen-containing extracellular matrix / angiogenesis / neuron apoptotic process / negative regulation of neuron apoptotic process / in utero embryonic development / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / membrane raft / positive regulation of gene expression / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
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: 2.098 Å
AuthorsYeykal, C.C. / Adams, E.J.
CitationJournal: To be Published
Title: Biochemical and structural characterization of the Ang1 fibrinogen-related domain
Authors: Yeykal, C.C. / Sundaresan, L. / Mrksich, M. / Adams, E.J.
History
DepositionApr 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Angiopoietin-1
B: Angiopoietin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6474
Polymers50,5672
Non-polymers802
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.903, 80.903, 186.087
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-805-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 1:215 )A1 - 215
211chain B and (resseq 1:215 )B1 - 215

-
Components

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


Mass: 25283.457 Da / Num. of mol.: 2
Fragment: Fibrinogen C-terminal domain, UNP residues 282-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANGPT1, KIAA0003 / Production host: Trichopulsia ni (cabbage looper) / References: UniProt: Q15389
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 3.48 Å3/Da / Density % sol: 64.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M PIPES pH 6.5, 0.2M NaCl, 2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 31, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.098→50 Å / Num. obs: 39116 / Observed criterion σ(I): -3

-
Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z3S

1z3s


Resolution: 2.098→46.443 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8492 / SU ML: 0.26 / σ(F): 0 / Phase error: 22.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2008 1873 5.03 %
Rwork0.1826 --
obs0.1835 37253 92.67 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.916 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso max: 147.92 Å2 / Biso mean: 37.4776 Å2 / Biso min: 14.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.899 Å2-0 Å2-0 Å2
2--0.899 Å20 Å2
3----1.7979 Å2
Refinement stepCycle: LAST / Resolution: 2.098→46.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 2 232 3706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073589
X-RAY DIFFRACTIONf_angle_d1.0754821
X-RAY DIFFRACTIONf_chiral_restr0.076460
X-RAY DIFFRACTIONf_plane_restr0.004629
X-RAY DIFFRACTIONf_dihedral_angle_d14.3181269
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1725X-RAY DIFFRACTIONPOSITIONAL0.015
12B1725X-RAY DIFFRACTIONPOSITIONAL0.015
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.098-2.15480.3465950.29311804189962
2.1548-2.21820.24641280.24512383251181
2.2182-2.28980.24981250.22682627275289
2.2898-2.37170.21341420.21952686282891
2.3717-2.46660.23961500.2042764291494
2.4666-2.57890.22641580.20792777293595
2.5789-2.71480.24441450.20222849299497
2.7148-2.88490.23471440.21872905304998
2.8849-3.10760.22881620.19742886304898
3.1076-3.42020.19811510.17962899305099
3.4202-3.91490.17251560.152926308299
3.9149-4.93150.14721850.129729093094100
4.9315-46.45470.19521320.18852965309799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0030.00120.00310.0029-0.00070.0016-0.0034-0.01410.0249-0.0051-0.012-0.0218-0.01780.0144-0.01610.4432-0.31940.10680.2741-0.13710.414415.758131.2887-9.3111
20.00710.0042-0.00910.0004-0.00150.0007-0.00780.00550.0514-0.02550.00210.0021-0.05110.0358-0.04690.3668-0.46630.14110.07430.05670.117611.520621.9331-20.4854
30.01760.00010.00580.00420.00860.01970.0159-0.0520.02170.0062-0.0011-0.0131-0.05110.0756-0.0040.3341-0.30820.02670.2666-0.11250.212611.02419.3008-9.6761
40.0050.0056-0.00570.02480.01790.03090.0065-0.00010.0325-0.0040.01280.004-0.07840.1226-0.00520.2455-0.13140.01840.2158-0.03780.0674.610212.754-11.3919
50.01910.012-00.00780.00470.00130.02310.0266-0.0339-0.05130.0404-0.0221-0.04560.03090.06680.2538-0.2899-0.04030.1801-0.06550.07419.21115.1559-20.991
60.00910.0031-0.03980.001-0.01020.21720.0141-0.0189-0.00450.0199-0.01130.00950.0022-0.0014-0.00290.3246-0.17940.00760.29230.00210.172-2.30238.8284-32.459
70.01720.0048-0.01870.0103-0.00280.03030.0159-0.02740.01990.0217-0.00210.0227-0.03350.02430.00370.3802-0.16420.02380.1636-0.01480.18210.135615.4077-17.9921
80.108-0.07430.02550.0515-0.01810.0075-0.0186-0.0359-0.0255-0.00550.0067-0.0801-0.00120.0614-0.00460.1131-0.04520.05850.6003-0.13410.448934.9281-2.26121.7418
90.0095-0.0167-0.00880.03510.02550.0202-0.0197-0.0055-0.0179-0.00170.0144-0.05830.0020.0097-0.01450.09420.0466-0.00360.4846-0.05050.259726.6352-7.08377.2138
100.07830.0110.04240.0076-0.00440.03410.02160.014-0.03760.01090.0215-0.03430.00010.064-0.00530.0478-0.0867-0.07190.5793-0.0630.163323.44493.482817.0971
110.0383-0.009-0.02240.01850.00290.0076-0.00250.0028-0.0006-0.03010.0443-0.025-0.04760.0980.00960.0811-0.08920.07170.5076-0.0530.226422.2246-0.10732.2576
120.0756-0.0062-0.01690.00220.00530.0091-0.0199-0.0308-0.01380.03450.0339-0.0485-0.07550.1564-0.00640.2155-0.04790.03530.414-0.02990.215515.4249-3.6135.7849
130.00790.00740.01970.02780.04870.0991-0.01530.03220.0007-0.0344-0.01690.0044-0.07470.07280.00370.1468-0.0512-0.01150.333-0.04510.066510.565-0.75111.5467
140.04420.0188-0.01560.0169-0.00260.03220.024-0.05550.0430.01930.04020.0252-0.01720.04540.06110.0626-0.0750.04930.42050.01760.08749.06415.396613.5681
150.15390.05450.08680.04540.07890.1443-0.00730.0577-0.0027-0.01130.0056-0.0022-0.00390.01550.00550.1765-0.07220.00390.41920.01040.18556.4896-6.405625.0394
160.0737-0.00230.01390.02740.01390.0127-0.00550.0312-0.0812-0.02150.0102-0.0002-0.00090.0460.01170.10180.00860.0040.448-0.02310.19813.4091-7.587510.5754
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 283:311)A283 - 311
2X-RAY DIFFRACTION2chain 'A' and (resseq 312:358)A312 - 358
3X-RAY DIFFRACTION3chain 'A' and (resseq 359:378)A359 - 378
4X-RAY DIFFRACTION4chain 'A' and (resseq 379:415)A379 - 415
5X-RAY DIFFRACTION5chain 'A' and (resseq 416:463)A416 - 463
6X-RAY DIFFRACTION6chain 'A' and (resseq 464:473)A464 - 473
7X-RAY DIFFRACTION7chain 'A' and (resseq 474:497)A474 - 497
8X-RAY DIFFRACTION8chain 'B' and (resseq 283:311)B283 - 311
9X-RAY DIFFRACTION9chain 'B' and (resseq 312:330)B312 - 330
10X-RAY DIFFRACTION10chain 'B' and (resseq 331:358)B331 - 358
11X-RAY DIFFRACTION11chain 'B' and (resseq 359:378)B359 - 378
12X-RAY DIFFRACTION12chain 'B' and (resseq 379:399)B379 - 399
13X-RAY DIFFRACTION13chain 'B' and (resseq 400:415)B400 - 415
14X-RAY DIFFRACTION14chain 'B' and (resseq 416:463)B416 - 463
15X-RAY DIFFRACTION15chain 'B' and (resseq 464:473)B464 - 473
16X-RAY DIFFRACTION16chain 'B' and (resseq 474:497)B474 - 497

+
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