[English] 日本語
Yorodumi
- PDB-9khc: Crystal structure of wild-type human fibrinogen gamma chain C-ter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9khc
TitleCrystal structure of wild-type human fibrinogen gamma chain C-terminal domain (gamma-nodule) complexed with GPRP peptide
Components
  • GLY-PRO-ARG-PRO
  • Isoform Gamma-A of Fibrinogen gamma chain
KeywordsBLOOD CLOTTING / fibrinogen / fibrin formation / hemostasis / coagulation factor
Function / homology
Function and homology information


fibrinogen complex / platelet alpha granule / Regulation of TLR by endogenous ligand / blood coagulation, fibrin clot formation / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / extracellular matrix structural constituent / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / plasminogen activation ...fibrinogen complex / platelet alpha granule / Regulation of TLR by endogenous ligand / blood coagulation, fibrin clot formation / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / extracellular matrix structural constituent / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / positive regulation of peptide hormone secretion / positive regulation of vasoconstriction / GRB2:SOS provides linkage to MAPK signaling for Integrins / protein secretion / positive regulation of exocytosis / protein polymerization / Integrin cell surface interactions / Common Pathway of Fibrin Clot Formation / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / fibrinolysis / cell adhesion molecule binding / Integrin signaling / positive regulation of substrate adhesion-dependent cell spreading / platelet alpha granule lumen / cell-matrix adhesion / positive regulation of protein secretion / Post-translational protein phosphorylation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / response to calcium ion / platelet aggregation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / Platelet degranulation / : / ER-Phagosome pathway / protein-containing complex assembly / blood microparticle / positive regulation of ERK1 and ERK2 cascade / endoplasmic reticulum lumen / signaling receptor binding / external side of plasma membrane / structural molecule activity / cell surface / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain ...Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile.
Similarity search - Domain/homology
Fibrinogen gamma chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsKaido, T. / Kamijo, T. / Arai, S. / Yamauchi, K. / Okumura, N. / Arai, R.
Funding support Japan, 5items
OrganizationGrant numberCountry
The Japanese Society of Hematology23135 Japan
Japan Society for the Promotion of Science (JSPS)JP20K07799 Japan
Japan Society for the Promotion of Science (JSPS)JP24K01267 Japan
Japan Society for the Promotion of Science (JSPS)JP19H02522 Japan
Japan Society for the Promotion of Science (JSPS)JP17KK0104 Japan
CitationJournal: To Be Published
Title: Crystal structure of wild-type human fibrinogen gamma chain C-terminal domain (gamma-nodule) complexed with GPRP peptide
Authors: Kaido, T. / Kamijo, T. / Arai, S. / Yamauchi, K. / Okumura, N. / Arai, R.
History
DepositionNov 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isoform Gamma-A of Fibrinogen gamma chain
B: GLY-PRO-ARG-PRO
C: Isoform Gamma-A of Fibrinogen gamma chain
D: GLY-PRO-ARG-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6818
Polymers62,4174
Non-polymers2644
Water7,386410
1
A: Isoform Gamma-A of Fibrinogen gamma chain
B: GLY-PRO-ARG-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2493
Polymers31,2092
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-12 kcal/mol
Surface area10290 Å2
MethodPISA
2
C: Isoform Gamma-A of Fibrinogen gamma chain
D: GLY-PRO-ARG-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4335
Polymers31,2092
Non-polymers2243
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-14 kcal/mol
Surface area10420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.897, 66.947, 91.428
Angle α, β, γ (deg.)90.000, 98.290, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Isoform Gamma-A of Fibrinogen gamma chain


Mass: 30782.014 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGG, PRO2061 / Plasmid: pPIC9K / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P02679
#2: Protein/peptide GLY-PRO-ARG-PRO


Mass: 426.490 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.99 % / Description: plate-like crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: The reservoir solution contains 0.1 M MES pH 6.0, 20% PEG8000, and 70 mM CaCl2. After clystals were grown, the reservoir solution containing 20 mM GPRP was added to the drop.

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 18, 2024 / Details: Focusing Mirror
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.32→45.24 Å / Num. obs: 100678 / % possible obs: 97.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 11.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.033 / Rrim(I) all: 0.088 / Χ2: 1.22 / Net I/σ(I): 14.9
Reflection shellResolution: 1.32→1.34 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 2 / Num. unique obs: 4925 / CC1/2: 0.63 / Rpim(I) all: 0.442 / Rrim(I) all: 1.16 / Χ2: 1.01

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→45.24 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.809 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.06
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 5054 5.022 %RANDOM
Rwork0.1694 95587 --
all0.171 ---
obs-100641 97.484 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.756 Å2
Baniso -1Baniso -2Baniso -3
1--0.934 Å2-0 Å2-0.094 Å2
2--1.948 Å20 Å2
3----0.946 Å2
Refinement stepCycle: LAST / Resolution: 1.32→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4034 0 14 410 4458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0124232
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.7955731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7195514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.488515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13210668
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.46710216
X-RAY DIFFRACTIONr_chiral_restr0.0830.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023460
X-RAY DIFFRACTIONr_nbd_refined0.2030.21933
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22849
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2368
X-RAY DIFFRACTIONr_metal_ion_refined0.0740.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2290.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1210.222
X-RAY DIFFRACTIONr_mcbond_it3.5771.6222044
X-RAY DIFFRACTIONr_mcangle_it5.6612.9132559
X-RAY DIFFRACTIONr_scbond_it3.7931.7582188
X-RAY DIFFRACTIONr_scangle_it5.883.1523171
X-RAY DIFFRACTIONr_lrange_it11.74620.1646750
X-RAY DIFFRACTIONr_rigid_bond_restr3.01134232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.3540.323590.3046899X-RAY DIFFRACTION96.1962
1.354-1.3910.2854010.2826648X-RAY DIFFRACTION94.6048
1.391-1.4320.2723740.2576444X-RAY DIFFRACTION94.7734
1.432-1.4760.2323470.2196458X-RAY DIFFRACTION96.2926
1.476-1.5240.223310.1986272X-RAY DIFFRACTION97.8947
1.524-1.5770.1872880.1726108X-RAY DIFFRACTION97.5446
1.577-1.6370.2122970.1625909X-RAY DIFFRACTION97.7323
1.637-1.7040.1933120.1595635X-RAY DIFFRACTION97.8447
1.704-1.7790.1832560.155522X-RAY DIFFRACTION98.0985
1.779-1.8660.1872760.1435223X-RAY DIFFRACTION98.3545
1.866-1.9670.1722750.1454980X-RAY DIFFRACTION98.5744
1.967-2.0860.1862430.1484739X-RAY DIFFRACTION98.7121
2.086-2.2290.1852570.1484419X-RAY DIFFRACTION98.6082
2.229-2.4080.1681860.1524043X-RAY DIFFRACTION95.6571
2.408-2.6370.1992240.1573830X-RAY DIFFRACTION99.023
2.637-2.9470.1911930.1583473X-RAY DIFFRACTION99.6466
2.947-3.40.1781530.1543118X-RAY DIFFRACTION99.5435
3.4-4.1580.21180.1422658X-RAY DIFFRACTION99.8921
4.158-5.8560.212970.1642049X-RAY DIFFRACTION99.814
5.856-45.240.26670.2211160X-RAY DIFFRACTION99.0315

+
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