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- PDB-3e1i: Crystal Structure of BbetaD432A Variant Fibrinogen Fragment D wit... -

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Basic information

Entry
Database: PDB / ID: 3e1i
TitleCrystal Structure of BbetaD432A Variant Fibrinogen Fragment D with the Peptide Ligand Gly-His-Arg-Pro-amide
Components
  • Fibrinogen alpha chain
  • Fibrinogen beta chain
  • Fibrinogen gamma chain
  • Gly-His-Arg-Pro-amide
KeywordsBLOOD CLOTTING / Blood Coagulation / Disease mutation / Glycoprotein / Phosphoprotein / Secreted / Pyrrolidone carboxylic acid / Sulfation
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 / protein secretion / positive regulation of exocytosis / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBowley, S.R. / Lord, S.T.
CitationJournal: Blood / Year: 2009
Title: Fibrinogen variant BbetaD432A has normal polymerization but does not bind knob "B".
Authors: Bowley, S.R. / Lord, S.T.
History
DepositionAug 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 18, 2013Group: Derived calculations
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description ...Data collection / Refinement description / Source and taxonomy / Structure summary
Category: entity / pdbx_entity_src_syn / software
Item: _entity.pdbx_fragment / _pdbx_entity_src_syn.details ..._entity.pdbx_fragment / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _software.classification / _software.name / _software.version
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _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 1.5Oct 20, 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 1.6Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Nov 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 chain
B: Fibrinogen beta chain
C: Fibrinogen gamma chain
D: Fibrinogen alpha chain
E: Fibrinogen beta chain
F: Fibrinogen gamma chain
G: Gly-His-Arg-Pro-amide
H: Gly-His-Arg-Pro-amide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,88617
Polymers169,1648
Non-polymers7239
Water4,684260
1
A: Fibrinogen alpha chain
B: Fibrinogen beta chain
C: Fibrinogen gamma chain
G: Gly-His-Arg-Pro-amide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9639
Polymers84,5824
Non-polymers3825
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-54 kcal/mol
Surface area27830 Å2
2
D: Fibrinogen alpha chain
E: Fibrinogen beta chain
F: Fibrinogen gamma chain
H: Gly-His-Arg-Pro-amide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9238
Polymers84,5824
Non-polymers3414
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8120 Å2
ΔGint-47 kcal/mol
Surface area27440 Å2
Unit cell
Length a, b, c (Å)54.476, 146.596, 228.960
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 chain / The peptide was chemically synthesized / Fibrinopeptide A


Mass: 10244.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGA / Plasmid: pMLP / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02671
#2: Protein Fibrinogen beta chain / Fibrinopeptide B


Mass: 37647.984 Da / Num. of mol.: 2 / Mutation: D432A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGB / Plasmid: pMLP / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02675
#3: Protein Fibrinogen gamma chain


Mass: 36223.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGG, PRO2061 / Plasmid: pMLP / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02679

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Protein/peptide / Sugars , 2 types, 4 molecules GH

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


Mass: 465.530 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: 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 , 2 types, 267 molecules

#6: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 50 mM Tris, 12.5 mM calcium chloride, 12% PEG 3350, 2 mM sodium azide, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97625 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 82662 / % possible obs: 83 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Net I/σ(I): 29.5
Reflection shellResolution: 2.15→2.28 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.284 / % possible all: 80.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LT9

1lt9


Resolution: 2.3→49.21 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.918 / SU B: 11.139 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / ESU R: 0.275 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24154 4129 5 %RANDOM
Rwork0.21436 ---
obs0.21573 78322 99.74 %-
all-100841 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.558 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--1.12 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10371 0 37 260 10668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210675
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0791.92914412
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66351283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74724.526548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.034151833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9681562
X-RAY DIFFRACTIONr_chiral_restr0.0780.21442
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028280
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.24786
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.27171
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2546
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0870.217
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5491.56576
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.975210194
X-RAY DIFFRACTIONr_scbond_it1.134870
X-RAY DIFFRACTIONr_scangle_it1.7414.54218
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 334 -
Rwork0.245 5678 -
obs--99.27 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3112-1.2551-2.60261.20262.347721.8871-0.6897-0.2125-0.5120.7708-0.00140.18271.73741.71050.6910.325-0.00310.00030.32730.14650.1616-13.8994-24.723385.1853
20.51020.13670.11670.74350.11411.35190.1138-0.21850.05220.074-0.1472-0.07580.0307-0.23530.0335-0.0494-0.0381-0.01470.2417-0.11350.0737-29.4115-19.690964.9391
30.26860.15450.14390.21340.33480.93550.0052-0.07650.0478-0.0299-0.02880.0070.04960.03380.02370.0550.0180.00440.0174-0.03210.1234-20.2497-25.521630.1743
43.1992-0.43380.98561.17-1.9553.2891-0.4718-0.58880.69260.41760.44380.2363-0.7597-0.22120.0280.28160.01670.12240.2884-0.10580.1052-4.9974-68.013670.7824
50.17450.38130.02271.04140.00910.72990.1982-0.27080.01370.0712-0.3557-0.03350.06960.02620.1575-0.0447-0.11920.010.27380.03310.06515.0563-55.168151.6991
60.6610.10080.42720.056-0.14231.3346-0.0091-0.0956-0.0616-0.1152-0.0824-0.01090.260.01790.09160.12420.0570.0554-0.03030.01660.1303-0.9312-63.485716.3381
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A134 - 190
2X-RAY DIFFRACTION2B161 - 458
3X-RAY DIFFRACTION3C105 - 392
4X-RAY DIFFRACTION4D134 - 187
5X-RAY DIFFRACTION5E161 - 458
6X-RAY DIFFRACTION6F106 - 393

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