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- PDB-2z4e: Crystal Structure of D-Dimer from Human Fibrin Complexed with Gly... -

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Basic information

Entry
Database: PDB / ID: 2z4e
TitleCrystal Structure of D-Dimer from Human Fibrin Complexed with Gly-His-Arg-Pro-Tyr-amide
Components
  • (Fibrin B knob ...) x 2
  • Fibrinogen alpha chain
  • Fibrinogen beta chain
  • Fibrinogen, gamma polypeptide
KeywordsBLOOD CLOTTING / fibrin clots / B-knobs / beta-holes
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 / MyD88 deficiency (TLR2/4) ...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 / 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 peptide hormone secretion / positive regulation of exocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / protein secretion / protein polymerization / cellular response to interleukin-1 / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / Common Pathway of Fibrin Clot Formation / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of vasoconstriction / cell adhesion molecule binding / fibrinolysis / 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) / Signaling by BRAF and RAF1 fusions / extracellular vesicle / Platelet degranulation / cell cortex / ER-Phagosome pathway / protein-folding chaperone binding / protein-containing complex assembly / collagen-containing extracellular matrix / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / blood microparticle / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / innate immune response / signaling receptor binding / 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 beta chain / Fibrinogen gamma chain / Fibrinogen gamma chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDoolittle, R.F. / Pandi, L.
CitationJournal: Biochemistry / Year: 2007
Title: Probing the beta-chain hole of fibrinogen with synthetic peptides that differ at their amino termini
Authors: Doolittle, R.F. / Pandi, L.
History
DepositionJun 16, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 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 / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type
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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300BIOMOLECULE: 1 The set of chains A-B-C is covalently cross-linked to the set D-E-F. But the cross- ...BIOMOLECULE: 1 The set of chains A-B-C is covalently cross-linked to the set D-E-F. But the cross-links (between a particular glutamine and a particular lysine in the C and F chains) occur in a part of the structure that doesn't appear in the electron density.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibrinogen alpha chain
B: Fibrinogen beta chain
C: Fibrinogen, gamma polypeptide
D: Fibrinogen alpha chain
E: Fibrinogen beta chain
F: Fibrinogen, gamma polypeptide
S: Fibrin B knob (tetrapeptide)
T: Fibrin B knob (tetrapeptide)
I: Fibrin B knob (pentapeptide)
J: Fibrin B knob (pentapeptide)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,13321
Polymers170,94510
Non-polymers1,18711
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Fibrinogen alpha chain
B: Fibrinogen beta chain
C: Fibrinogen, gamma polypeptide
S: Fibrin B knob (tetrapeptide)
I: Fibrin B knob (pentapeptide)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,05710
Polymers85,4735
Non-polymers5855
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11060 Å2
ΔGint-104 kcal/mol
Surface area27950 Å2
MethodPISA
3
D: Fibrinogen alpha chain
E: Fibrinogen beta chain
F: Fibrinogen, gamma polypeptide
T: Fibrin B knob (tetrapeptide)
J: Fibrin B knob (pentapeptide)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,07511
Polymers85,4735
Non-polymers6036
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10280 Å2
ΔGint-99 kcal/mol
Surface area26520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.630, 148.690, 232.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 chain


Mass: 10244.963 Da / Num. of mol.: 2 / Fragment: residues in database 130-218 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02671
#2: Protein Fibrinogen beta chain


Mass: 37435.730 Da / Num. of mol.: 2 / Fragment: residues in database 164-491 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02675
#3: Protein Fibrinogen, gamma polypeptide


Mass: 36693.754 Da / Num. of mol.: 2 / Fragment: residues in database 114-437 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q53Y18, UniProt: P02679*PLUS

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Fibrin B knob ... , 2 types, 4 molecules STIJ

#4: Protein/peptide Fibrin B knob (tetrapeptide)


Mass: 467.522 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The sequence occurs naturally in humans.
#5: Protein/peptide Fibrin B knob (pentapeptide)


Mass: 630.696 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The sequence occurs naturally in bovines (e.g., Bos taurus).
References: UniProt: P02676*PLUS

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Sugars , 2 types, 3 molecules

#6: 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.: 1
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
#8: 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: 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 , 1 types, 8 molecules

#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca

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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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: equal volumes of (a) 9 mg/ml D-dimer, 2mM Gly-His-Arg-Pro-amide, 0.05M Tris, pH 7.0, 5mM CaCl2; (b) 10% PEG, 5mM CaCl2, 0.05M Tris, pH 8.0, 2mM sodium azide; The crystal was subsequently ...Details: equal volumes of (a) 9 mg/ml D-dimer, 2mM Gly-His-Arg-Pro-amide, 0.05M Tris, pH 7.0, 5mM CaCl2; (b) 10% PEG, 5mM CaCl2, 0.05M Tris, pH 8.0, 2mM sodium azide; The crystal was subsequently soaked in 0.5mM Gly-His-Arg-Pro-Tyr-amide in solution of came constitution., pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 8, 2006 / Details: superbend
RadiationMonochromator: single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.66→50 Å / Num. all: 56549 / Num. obs: 55743 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.7 % / Rsym value: 0.071 / Net I/σ(I): 14.4
Reflection shellResolution: 2.66→2.76 Å / Redundancy: 7.9 % / Rsym value: 0.294 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FZF

1fzf


Resolution: 2.7→30 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.275 --Random
Rwork0.216 ---
all0.22 53173 --
obs0.2177 51522 96.9 %-
Solvent computationBsol: 24.122 Å2
Displacement parametersBiso mean: 40.916 Å2
Baniso -1Baniso -2Baniso -3
1-1.965 Å20 Å20 Å2
2---11.105 Å20 Å2
3---9.14 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10581 0 65 0 10646
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.348
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2carbohydrate.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4cis_peptide.param

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