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- PDB-3h32: Crystal structure of D-dimer from human fibrin complexed with Gly... -

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Basic information

Entry
Database: PDB / ID: 3h32
TitleCrystal structure of D-dimer from human fibrin complexed with Gly-His-Arg-Pro-Tyr-amide
Components
  • Fibrin B knob pentapeptide
  • Fibrinogen alpha chain
  • Fibrinogen beta chain
  • Fibrinogen gamma chain, isoform gamma-A
KeywordsBLOOD CLOTTING / fibrinogen / fibrin clots / Amyloid / Amyloidosis / Blood coagulation / Disease mutation / Disulfide bond / Glycoprotein / Isopeptide bond / Phosphoprotein / Secreted / Pyrrolidone carboxylic acid / Sulfation / cDNA FLJ75335 / transcript variant gamma-A / mRNA / isoform CRA_m
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 beta chain / Fibrinogen gamma chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsDoolittle, R.F. / Pandi, L.
CitationJournal: Biochemistry / Year: 2009
Title: Two families of synthetic peptides that enhance fibrin turbidity and delay fibrinolysis by different mechanisms.
Authors: Pandi, L. / Kollman, J.M. / Lopez-Lira, F. / Burrows, J.M. / Riley, M. / Doolittle, R.F.
History
DepositionApr 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 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_validate_chiral / 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.ptnr2_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_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.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 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

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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 chain, isoform gamma-A
D: Fibrinogen alpha chain
E: Fibrinogen beta chain
F: Fibrinogen gamma chain, isoform gamma-A
M: Fibrin B knob pentapeptide
N: Fibrin B knob pentapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,78714
Polymers222,4928
Non-polymers3,2956
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22010 Å2
ΔGint-144 kcal/mol
Surface area57610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)264.720, 97.320, 132.490
Angle α, β, γ (deg.)90.00, 122.78, 90.00
Int Tables number5
Space group name H-MC121
DetailsD-DIMER IS COMPOSED OF TWO (IDENTICAL) THREE-CHAINED MOIETIES CROSS-LINKED NEAR THE CARBOXYL-TERMINI OF THE GAMMA CHAINS.

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein Fibrinogen alpha chain / / Fibrinopeptide A


Mass: 22771.676 Da / Num. of mol.: 2 / Fragment: UNP residues 20-216 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: blood plasma / References: UniProt: P02671
#2: Protein Fibrinogen beta chain / / Fibrinopeptide B


Mass: 52026.066 Da / Num. of mol.: 2 / Fragment: UNP residues 31-488 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: blood plasma / References: UniProt: P02675
#3: Protein Fibrinogen gamma chain, isoform gamma-A /


Mass: 35817.645 Da / Num. of mol.: 2 / Fragment: UNP residues 27-437 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: blood plasma / References: UniProt: P02679

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Protein/peptide / Sugars / Non-polymers , 3 types, 8 molecules MN

#4: Protein/peptide Fibrin B knob pentapeptide


Mass: 630.696 Da / Num. of mol.: 2 / Fragment: UNP residues 22-26 / Source method: obtained synthetically
Details: Synthetic peptide based on the bovine (Bos taurus) Fibrinopeptide B, P02676, FIBB_BOVIN, sequence position 22-26
References: UniProt: P02676
#5: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1567.411 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-2DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-1-2-2-1-3-4-2/a4-b1_b4-c1_c3-d1_c6-h1_d2-e1_e4-f1_f6-g2WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / 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: 3.22 Å3/Da / Density % sol: 61.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Equal volumes of (a) 5 mg/mL D-dimer, 0.5 mM GHRPYam, 0.3 mM GPRPam, 0.05 M Tris-HCl pH 8.0 and (b) 1% PEG 3350, 1 mM Iodoacetamide, 1 mM CaCl2, 2mM Sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2007
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. all: 33100 / Num. obs: 31584 / % possible obs: 95 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rsym value: 0.073

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FZE

1fze


Resolution: 3.6→50 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.3199 1244 -random
Rwork0.2631 ---
obs0.2631 25002 75.5 %-
all-31584 --
Refinement stepCycle: LAST / Resolution: 3.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11030 0 216 0 11246
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.679
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsTotal num. of bins used% reflection obs (%)
3.6-3.73X-RAY DIFFRACTION2582678.2
3.73-3.88X-RAY DIFFRACTION2945689.2
3.88-4.05X-RAY DIFFRACTION3106694.5
4.05-4.27X-RAY DIFFRACTION3159695.6
4.27-4.53X-RAY DIFFRACTION3181696.3
4.53-4.88X-RAY DIFFRACTION3190696.3

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