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- PDB-1fzd: STRUCTURE OF RECOMBINANT ALPHAEC DOMAIN FROM HUMAN FIBRINOGEN-420 -

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Basic information

Entry
Database: PDB / ID: 1fzd
TitleSTRUCTURE OF RECOMBINANT ALPHAEC DOMAIN FROM HUMAN FIBRINOGEN-420
ComponentsFIBRINOGEN-420
KeywordsBLOOD COAGULATION / FIBRINOGEN-420 / ALPHAEC DOMAIN / FIBRINOGEN RELATED DOMAIN / GLYCOSYLATED PROTEIN
Function / homology
Function and homology information


blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / positive regulation of heterotypic cell-cell adhesion / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) / extracellular matrix structural constituent ...blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / 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 / GRB2:SOS provides linkage to MAPK signaling for Integrins / 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 / positive regulation of vasoconstriction / fibrinolysis / 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 / 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 / ER-Phagosome pathway / protein-containing complex assembly / : / blood microparticle / protein-macromolecule adaptor activity / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / Amyloid fiber formation / endoplasmic reticulum lumen / signaling receptor binding / innate immune response / external side of plasma membrane / structural molecule activity / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
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 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. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Fibrinogen alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSpraggon, G. / Applegate, D. / Everse, S.J. / Zhang, J.-Z. / Veerapandian, L. / Redman, C. / Doolittle, R.F. / Grieninger, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Crystal structure of a recombinant alphaEC domain from human fibrinogen-420.
Authors: Spraggon, G. / Applegate, D. / Everse, S.J. / Zhang, J.Z. / Veerapandian, L. / Redman, C. / Doolittle, R.F. / Grieninger, G.
History
DepositionJun 22, 1998Processing site: BNL
Revision 1.0Aug 19, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Advisory / Database references ...Advisory / Database references / Refinement description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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-420
B: FIBRINOGEN-420
C: FIBRINOGEN-420
D: FIBRINOGEN-420
E: FIBRINOGEN-420
F: FIBRINOGEN-420
G: FIBRINOGEN-420
H: FIBRINOGEN-420
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,23626
Polymers182,7258
Non-polymers6,51018
Water8,935496
1
A: FIBRINOGEN-420
B: FIBRINOGEN-420
C: FIBRINOGEN-420
D: FIBRINOGEN-420
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,97912
Polymers91,3634
Non-polymers4,6168
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: FIBRINOGEN-420
F: FIBRINOGEN-420
G: FIBRINOGEN-420
H: FIBRINOGEN-420
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,25714
Polymers91,3634
Non-polymers1,89410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.250, 105.180, 71.140
Angle α, β, γ (deg.)104.60, 108.95, 71.47
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99581, 0.09124, 0.00591), (-0.09143, 0.99452, 0.05068), (-0.00126, -0.051, 0.9987)32.93274, -1.95952, 1.04752
2given(0.9918, 0.12739, 0.00981), (0.12723, -0.99176, 0.01507), (0.01165, -0.0137, -0.99984)14.53325, 36.88934, 30.61141
3given(0.97852, 0.20558, -0.01529), (0.20583, -0.97844, 0.01703), (-0.01146, -0.01981, -0.99974)48.01752, 39.69883, 30.09678
4given(-0.99997, 0.0073, 0.00061), (-0.00732, -0.9977, -0.06741), (0.00012, -0.06741, 0.99773)51.1767, 85.3503, 2.91451
5given(-0.99613, -0.08704, -0.01187), (0.08784, -0.98797, -0.12729), (-0.00065, -0.12784, 0.99179)89.68814, 87.21141, 4.03518
6given(-0.99398, -0.10954, -0.00226), (-0.10953, 0.99297, 0.04489), (-0.00268, 0.04487, -0.99899)36.30933, 46.88599, 30.9222
7given(-0.98342, -0.17712, 0.03879), (-0.17459, 0.98275, 0.06107), (-0.04894, 0.05328, -0.99738)73.74581, 43.85368, 29.40255

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
FIBRINOGEN-420


Mass: 22840.660 Da / Num. of mol.: 8 / Fragment: ALPHA-EC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: BLOOD / Production host: Pichia pastoris (fungus) / References: UniProt: P02671

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Sugars , 4 types, 10 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1114.016 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-1/a4-b1_b4-c1_c3-d1_c6-e1_e2-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1114.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpa1-4DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-2-3-3-3-1/a4-b1_b4-c1_c3-d1_c6-e1_e2-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Rhap]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: 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.: 4
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 2 types, 504 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 496 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 50 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.5
Details: PROTEIN WAS CRYSTALLIZED BY SITTING DROP VAPOUR DIFFUSION FROM 20% PEG 3350, 0.15 M CACL2, 0.1M IMIDAZOLE- ACETATE PH 5.5 0.002 M SODIUM AZIDE, vapor diffusion - sitting drop
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %PEG33501reservoir
20.15 M1reservoirCaCl2
30.1 Mimidazole acetate1reservoir
40.002 Msodium azide1reservoir
58 mg/mlprotain1drop
60.02 MTris1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.08
DetectorDetector: CCD / Date: Feb 20, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 110459 / % possible obs: 91.2 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.098
Reflection
*PLUS
Num. measured all: 1169328

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Processing

Software
NameClassification
SCALEPACKdata scaling
X-PLORmodel building
REFMACrefinement
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FCZ (GAMMA DOMAIN)

1fcz


Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: CARBOHYDRATE RESIDUES 12 - 15 FOR CHAINS A, B, C, AND D WERE MODELLED INTO WEAK ELECTRON DENSITY. THERE WAS NO ELECTRON DENSITY OBSERVED FOR THESE RESIDUES IN CHAINS E, F, G, AND H.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 5530 5 %RANDOM
Rwork0.195 ---
obs0.199 110459 91.2 %-
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12680 0 419 496 13595
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d3
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d27.5
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.98
X-RAY DIFFRACTIONp_mcangle_it3.7
X-RAY DIFFRACTIONp_scbond_it5.1
X-RAY DIFFRACTIONp_scangle_it6.53
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr3
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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