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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ltj
TitleCrystal Structure of Recombinant Human Fibrinogen Fragment D with the Peptide Ligands Gly-Pro-Arg-Pro-Amide and Gly-His-Arg-Pro-Amide
Components
  • Fibrinogen Beta chain
  • Fibrinogen Gamma chain
  • Fibrinogen alpha/alpha-E chain
  • Gly-His-Arg-Pro
  • Gly-Pro-Arg-Pro
KeywordsBLOOD CLOTTING / blood coagulation / fibrinogen / fibrinogen fragment D / recombinant fibrinogen fragment D / recombinant fibrinogen / recombinant fibrinogen fragment D with two peptide ligands
Function / homology
Function and homology information


platelet maturation / blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / blood coagulation, fibrin clot formation / platelet alpha granule / cellular response to leptin stimulus / cellular response to interleukin-6 / MyD88 deficiency (TLR2/4) ...platelet maturation / blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / blood coagulation, fibrin clot formation / platelet alpha granule / cellular response to leptin stimulus / cellular response to interleukin-6 / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extracellular matrix structural constituent / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / positive regulation of exocytosis / positive regulation of peptide hormone secretion / GRB2:SOS provides linkage to MAPK signaling for Integrins / protein secretion / protein polymerization / Integrin cell surface interactions / cellular response to interleukin-1 / negative regulation of endothelial cell apoptotic process / Common Pathway of Fibrin Clot Formation / positive regulation of substrate adhesion-dependent cell spreading / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of vasoconstriction / fibrinolysis / cell adhesion molecule binding / Integrin signaling / cell-matrix adhesion / platelet alpha granule lumen / 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 / 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 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / extracellular vesicle / Signaling by BRAF and RAF1 fusions / Platelet degranulation / cell cortex / ER-Phagosome pathway / protein-folding chaperone binding / protein-containing complex assembly / collagen-containing extracellular matrix / blood microparticle / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / Amyloid fiber formation / external side of plasma membrane / endoplasmic reticulum lumen / signaling receptor binding / innate immune response / synapse / structural molecule activity / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding / metal ion 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 chain / 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 ...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 chain / 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, 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. / 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_label_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_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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

-
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
G: Gly-Pro-Arg-Pro
H: Gly-His-Arg-Pro
I: Gly-Pro-Arg-Pro
J: Gly-His-Arg-Pro
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,90016
Polymers159,59810
Non-polymers1,3016
Water4,504250
1
A: Fibrinogen alpha/alpha-E chain
B: Fibrinogen Beta chain
C: Fibrinogen Gamma chain
G: Gly-Pro-Arg-Pro
H: Gly-His-Arg-Pro
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4508
Polymers79,7995
Non-polymers6513
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11380 Å2
ΔGint-74 kcal/mol
Surface area27560 Å2
MethodPISA
2
D: Fibrinogen alpha/alpha-E chain
E: Fibrinogen Beta chain
F: Fibrinogen Gamma chain
I: Gly-Pro-Arg-Pro
J: Gly-His-Arg-Pro
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4508
Polymers79,7995
Non-polymers6513
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.284, 94.218, 226.936
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

-
Protein/peptide , 2 types, 4 molecules GIHJ

#4: Protein/peptide Gly-Pro-Arg-Pro


Mass: 426.490 Da / Num. of mol.: 2 / Source method: obtained synthetically
#5: Protein/peptide Gly-His-Arg-Pro


Mass: 467.522 Da / Num. of mol.: 2 / Source method: obtained synthetically

-
Sugars , 1 types, 2 molecules

#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

-
Non-polymers , 2 types, 254 molecules

#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 7% PEG 3350, 12.5mM Calcium Chloride, 2mM Sodium Azide, 50mM Tris pH 8.5, 2mM GHRP-amide, 2mM GPRP-amide, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
250 mMTris1droppH7.0
32 mMGHRPam1drop
42 mMGPRPam1drop
550 mMTris1reservoirpH8.5
62 mM1reservoirNaN3
712.5 mM1reservoirCaCl2
87 %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: Nov 9, 2001 / Details: Osmic Confocal Blue Multilayer Optics
RadiationProtocol: 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: 46717 / Num. obs: 46717 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 72.1 Å2 / Rsym value: 0.123 / Net I/σ(I): 13.8
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 2.9 / Num. unique all: 4355 / Rsym value: 0.393 / % possible all: 92.8
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 18 Å / Num. measured all: 181953 / Rmerge(I) obs: 0.123
Reflection shell
*PLUS
% possible obs: 92.8 % / Rmerge(I) obs: 0.393

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FZC

1fzc


Resolution: 2.8→18.02 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
Rfree0.27 2364 5.1 %RANDOM
Rwork0.212 ---
all-46668 --
obs-46668 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.0545 Å2 / ksol: 0.33163 e/Å3
Displacement parametersBiso mean: 45 Å2
Baniso -1Baniso -2Baniso -3
1-10.99 Å20 Å20 Å2
2---4.62 Å20 Å2
3----6.36 Å2
Refine analyzeLuzzati coordinate error free: 0.43 Å / Luzzati sigma a free: 0.5 Å
Refinement stepCycle: LAST / Resolution: 2.8→18.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10563 0 80 250 10893
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.378 376 5.2 %
Rwork0.299 6876 -
obs-7252 91.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CIS_PEPTIDE.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAM
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 18 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0066
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

+
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