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- PDB-9khb: Crystal structure of wild-type human fibrinogen gamma chain C-ter... -

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Basic information

Entry
Database: PDB / ID: 9khb
TitleCrystal structure of wild-type human fibrinogen gamma chain C-terminal domain (gamma-nodule)
ComponentsIsoform 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: 1.03 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)
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform Gamma-A of Fibrinogen gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0985
Polymers30,7821
Non-polymers3164
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.797, 66.656, 46.564
Angle α, β, γ (deg.)90.000, 105.177, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 30782.014 Da / Num. of mol.: 1
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.09 % / Description: plate-like crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Reservoir solution (22% PEG 8000, 150 mM 2-Morpholinoethanesulfonic acid, pH 6.0, 70 mM calcium choride) Protein solution (20 mM 2-[4-(2-Hydroxyethyl)-1-piperazinyl]ethanesulfonic acid, pH7. ...Details: Reservoir solution (22% PEG 8000, 150 mM 2-Morpholinoethanesulfonic acid, pH 6.0, 70 mM calcium choride) Protein solution (20 mM 2-[4-(2-Hydroxyethyl)-1-piperazinyl]ethanesulfonic acid, pH7.4, 120 mM sodium choride, 70 mM calcium choride)

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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: Dec 16, 2023 / 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: 1.03→44.94 Å / Num. obs: 103954 / % possible obs: 97.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 10.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.021 / Rrim(I) all: 0.054 / Χ2: 0.95 / Net I/σ(I): 17.4
Reflection shellResolution: 1.03→1.05 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.714 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4920 / CC1/2: 0.828 / Rpim(I) all: 0.298 / Rrim(I) all: 0.776 / Χ2: 0.66 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.03→44.94 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.68 / SU ML: 0.015 / Cross valid method: FREE R-VALUE / ESU R: 0.022 / ESU R Free: 0.023
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.1388 5116 4.923 %
Rwork0.1193 98806 -
all0.12 --
obs-103922 97.254 %
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: 13.445 Å2
Baniso -1Baniso -2Baniso -3
1--0.395 Å2-0 Å2-0.196 Å2
2--0.84 Å2-0 Å2
3----0.295 Å2
Refinement stepCycle: LAST / Resolution: 1.03→44.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 19 284 2305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122236
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162033
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.7963033
X-RAY DIFFRACTIONr_angle_other_deg0.651.8044621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6575279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.71156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.21510360
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.1210113
X-RAY DIFFRACTIONr_chiral_restr0.0940.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022753
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02574
X-RAY DIFFRACTIONr_nbd_refined0.2040.2397
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.21907
X-RAY DIFFRACTIONr_nbtor_refined0.190.21083
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21177
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2180
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1650.29
X-RAY DIFFRACTIONr_nbd_other0.2060.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1950.233
X-RAY DIFFRACTIONr_mcbond_it2.7941.1151078
X-RAY DIFFRACTIONr_mcbond_other2.7721.1131076
X-RAY DIFFRACTIONr_mcangle_it4.0662.0041367
X-RAY DIFFRACTIONr_mcangle_other4.0692.0061368
X-RAY DIFFRACTIONr_scbond_it3.8131.2941158
X-RAY DIFFRACTIONr_scbond_other3.8121.2951159
X-RAY DIFFRACTIONr_scangle_it5.522.281666
X-RAY DIFFRACTIONr_scangle_other5.5192.2821667
X-RAY DIFFRACTIONr_lrange_it9.04515.8792636
X-RAY DIFFRACTIONr_lrange_other8.23513.2232570
X-RAY DIFFRACTIONr_rigid_bond_restr3.15234269
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.03-1.0570.2033700.19170060.19279050.970.97393.3080.166
1.057-1.0860.183730.17168710.17176610.9770.97994.55680.143
1.086-1.1170.1683310.15368040.15374540.980.98395.72040.125
1.117-1.1510.1373600.12866310.12972600.9870.98996.29480.105
1.151-1.1890.1433540.11864610.11970490.9870.99196.68040.097
1.189-1.2310.1263050.11562920.11667960.9890.99197.07180.095
1.231-1.2770.1223060.10560950.10665720.9910.99397.39810.087
1.277-1.3290.1233040.10258630.10363140.9910.99397.67180.086
1.329-1.3890.1172940.09756220.09860400.9910.99497.9470.082
1.389-1.4560.1152650.09554310.09658110.9910.99498.0210.084
1.456-1.5350.1262660.09551920.09655420.990.99598.48430.087
1.535-1.6280.12610.09248560.09351960.9940.99598.47960.088
1.628-1.740.1272220.09846530.09949340.9910.99498.80420.096
1.74-1.8790.1332200.10742910.10845580.990.99398.96880.108
1.879-2.0580.1392030.11139860.11342290.9890.99299.05420.119
2.058-2.3010.1231810.10935940.1138320.990.99398.51250.122
2.301-2.6550.1431740.12431530.12533510.9870.99199.28380.145
2.655-3.2490.1491450.12926990.1328570.9860.9999.5450.158
3.249-4.5830.1571210.12421090.12622320.9860.99199.91040.158
4.583-44.940.163610.1811970.17912630.9870.98499.60410.238

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