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- PDB-1rf1: Crystal Structure of Fragment D of gammaE132A Fibrinogen with the... -

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Basic information

Entry
Database: PDB / ID: 1rf1
TitleCrystal Structure of Fragment D of gammaE132A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-amide
Components
  • Fibrinogen alpha/alpha-E chain
  • Fibrinogen beta chain
  • Fibrinogen gamma chain
  • GHRP peptide
KeywordsBLOOD CLOTTING / BLOOD COAGULATION / FIBRINOGEN / FIBRINOGEN FRAGMENT D / RECOMBINANT FIBRINOGEN FRAGMENT D / fragment D of gammaE132A / FIBRINOGEN with GHRP-amide
Function / homology
Function and homology information


blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / platelet alpha granule / Regulation of TLR by endogenous ligand / blood coagulation, fibrin clot formation / cellular response to leptin stimulus / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) ...blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / platelet alpha granule / Regulation of TLR by endogenous ligand / blood coagulation, fibrin clot formation / cellular response to leptin stimulus / 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 / positive regulation of exocytosis / protein secretion / protein polymerization / cellular response to interleukin-1 / 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 / extracellular vesicle / protein-folding chaperone binding / : / ER-Phagosome pathway / protein-containing complex assembly / cell cortex / protein-macromolecule adaptor activity / blood microparticle / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / innate immune response / external side of plasma membrane / synapse / structural molecule activity / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / 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/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 / SYNCHROTRON / rigid body refinement / Resolution: 2.53 Å
AuthorsKostelansky, M.S. / Gorkun, O.V. / Lord, S.T.
CitationJournal: Biochemistry / Year: 2004
Title: Calcium-Binding Site beta2, Adjacent to the "b" Polymerization Site, Modulates Lateral Aggregation of Protofibrils during Fibrin Polymerization.
Authors: Kostelansky, M.S. / Lounes, K.C. / Ping, L.F. / Dickerson, S.K. / Gorkun, O.V. / Lord, S.T.
History
DepositionNov 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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_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 2.1Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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: GHRP peptide
H: GHRP peptide
I: GHRP peptide
J: GHRP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,86616
Polymers159,56410
Non-polymers1,3016
Water4,468248
1
A: Fibrinogen alpha/alpha-E chain
B: Fibrinogen beta chain
C: Fibrinogen gamma chain
G: GHRP peptide
H: GHRP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4338
Polymers79,7825
Non-polymers6513
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-73 kcal/mol
Surface area27850 Å2
MethodPISA
2
D: Fibrinogen alpha/alpha-E chain
E: Fibrinogen beta chain
F: Fibrinogen gamma chain
I: GHRP peptide
J: GHRP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4338
Polymers79,7825
Non-polymers6513
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.714, 94.683, 228.198
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein Fibrinogen alpha/alpha-E chain


Mass: 7747.030 Da / Num. of mol.: 2 / Fragment: Fibrinogen alpha/alpha-E Chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGA / Plasmid: p767 / Cell line (production host): CHO / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02671
#2: Protein Fibrinogen beta chain


Mass: 35940.215 Da / Num. of mol.: 2 / Fragment: Fibrinogen Bbeta Chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGB / Plasmid: p767 / Cell line (production host): CHO / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02675
#3: Protein Fibrinogen gamma chain / PRO2061


Mass: 35159.957 Da / Num. of mol.: 2 / Fragment: Fibrinogen gamma chain / Mutation: E132A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGG / Plasmid: p767 / Cell line (production host): CHO / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02679

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Protein/peptide / Sugars , 2 types, 6 molecules GHIJ

#4: Protein/peptide
GHRP peptide


Mass: 467.522 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#5: 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

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Non-polymers , 2 types, 252 molecules

#6: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.04 Å3/Da / Density % sol: 59.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 9-10% PEG 3350, 12.5 mM calcium chloride, 2 mM sodium azide, 50 mM Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
250 mMTris1droppH7.4
32 mMGHRPam1drop
450 mMTris1reservoirpH8.5
52 mM1reservoirNaN3
612.5 mM1reservoirCaCl2
79-10 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98396 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 12, 2003
Details: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing)
RadiationMonochromator: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98396 Å / Relative weight: 1
ReflectionResolution: 2.53→18 Å / Num. obs: 66025 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 33.8 Å2 / Rsym value: 0.09 / Net I/σ(I): 13.8
Reflection shellResolution: 2.53→2.62 Å / Mean I/σ(I) obs: 4 / Num. unique all: 6506 / Rsym value: 0.359 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 18 Å / Num. measured all: 264892 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.359

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: rigid body refinement
Starting model: pdb entry 1LTJ

1ltj


Resolution: 2.53→17.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2084524.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 3316 5.1 %RANDOM
Rwork0.234 ---
obs0.234 65460 99.9 %-
all-65460 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.1769 Å2 / ksol: 0.333272 e/Å3
Displacement parametersBiso mean: 38.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.38 Å20 Å20 Å2
2---2.06 Å20 Å2
3----6.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.53→17.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10600 0 80 248 10928
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 2.53→2.69 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.364 545 5.1 %
Rwork0.309 10241 -
obs--100 %
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
Lowest resolution: 18 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0064
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

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