[English] 日本語
Yorodumi
- PDB-1lt9: Crystal Structure of Recombinant Human Fibrinogen Fragment D -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lt9
TitleCrystal Structure of Recombinant Human Fibrinogen Fragment D
Components
  • Fibrinogen alpha/alpha-E chain
  • Fibrinogen beta chain
  • Fibrinogen gamma chain
KeywordsBLOOD CLOTTING / blood coagulation / fibrinogen / fibrinogen fragment D / recombinant fibrinogen fragment D / recombinant fibrinogen
Function / homology
Function and homology information


platelet maturation / blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to leptin stimulus / cellular response to interleukin-6 / positive regulation of heterotypic cell-cell adhesion ...platelet maturation / blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to leptin stimulus / cellular response to interleukin-6 / positive regulation of heterotypic cell-cell adhesion / MyD88 deficiency (TLR2/4) / 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 exocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / protein secretion / cellular response to interleukin-1 / 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 / positive regulation of vasoconstriction / positive regulation of substrate adhesion-dependent cell spreading / Integrin signaling / 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 / platelet aggregation / response to calcium ion / 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 / extracellular vesicle / protein-folding chaperone binding / ER-Phagosome pathway / cell cortex / protein-containing complex assembly / protein-macromolecule adaptor activity / : / blood microparticle / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / signaling receptor binding / innate immune response / synapse / structural molecule activity / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #50 / Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #50 / Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / 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 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. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Few Secondary Structures / Irregular / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Fibrinogen alpha chain / Fibrinogen beta chain / Fibrinogen gamma chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKostelansky, M.S. / Betts, L. / Gorkun, O.V. / Lord, S.T.
CitationJournal: Biochemistry / Year: 2002
Title: 2.8 A Crystal Structures of Recombinant Fibrinogen Fragment D with and without Two Peptide Ligands: GHRP Binding to the "b" Site Disrupts Its Nearby Calcium-binding Site.
Authors: Kostelansky, M.S. / Betts, L. / Gorkun, O.V. / Lord, S.T.
History
DepositionMay 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fibrinogen alpha/alpha-E chain
B: Fibrinogen beta chain
C: Fibrinogen gamma chain
D: Fibrinogen alpha/alpha-E chain
E: Fibrinogen beta chain
F: Fibrinogen gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,49314
Polymers157,8106
Non-polymers6838
Water2,630146
1
A: Fibrinogen alpha/alpha-E chain
B: Fibrinogen beta chain
C: Fibrinogen gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2477
Polymers78,9053
Non-polymers3414
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9720 Å2
ΔGint-89 kcal/mol
Surface area27520 Å2
MethodPISA
2
D: Fibrinogen alpha/alpha-E chain
E: Fibrinogen beta chain
F: Fibrinogen gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2477
Polymers78,9053
Non-polymers3414
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-86 kcal/mol
Surface area26560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.727, 94.511, 227.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 3 types, 6 molecules ADBECF

#1: Protein Fibrinogen alpha/alpha-E chain


Mass: 7747.030 Da / Num. of mol.: 2 / Fragment: Fragment D (residues 126-191)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO Cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02671
#2: Protein Fibrinogen beta chain


Mass: 35940.215 Da / Num. of mol.: 2 / Fragment: Fragment D (residues 149-461)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO Cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02675
#3: Protein Fibrinogen gamma chain


Mass: 35217.992 Da / Num. of mol.: 2 / Fragment: Fragment D (residues 96-406)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO Cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02679

-
Sugars , 1 types, 2 molecules

#4: 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: obtained synthetically / 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

-
Non-polymers , 2 types, 152 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 9% PEG 3350, 70mM Calcium Chloride, 2mM Sodium Azide, 50mM Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
350 mMTris1reservoirpH8.5
42 mM1reservoirNaN3
570 mM1reservoirCaCl2
69 %(w/v)PEG33501reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 27, 2001 / Details: Osmic Confocal Blue Multilayer Optics
RadiationMonochromator: Osmic Confocal Blue Multilayer Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→18 Å / Num. all: 47742 / Num. obs: 47742 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 70.6 Å2 / Rsym value: 0.11 / Net I/σ(I): 14
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 3.1 / Num. unique all: 4684 / Rsym value: 0.54 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 18 Å / Num. measured all: 217604 / Rmerge(I) obs: 0.11
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.54

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→17.98 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2415 5.1 %RANDOM
Rwork0.224 ---
all-47606 --
obs-47606 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.6846 Å2 / ksol: 0.30323 e/Å3
Displacement parametersBiso mean: 47.2 Å2
Baniso -1Baniso -2Baniso -3
1-14.98 Å20 Å20 Å2
2---4.63 Å20 Å2
3----10.34 Å2
Refine analyzeLuzzati coordinate error free: 0.44 Å / Luzzati sigma a free: 0.48 Å
Refinement stepCycle: LAST / Resolution: 2.8→17.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10437 0 34 146 10617
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 409 5.2 %
Rwork0.313 7432 -
obs-7841 99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CIS_PEPTIDE.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAM
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0068
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

+
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