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- PDB-1lwu: Crystal structure of fragment D from lamprey fibrinogen complexed... -

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Basic information

Entry
Database: PDB / ID: 1lwu
TitleCrystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide
Components
  • Fibrinogen alpha-1 chain
  • Fibrinogen beta chain
  • Fibrinogen gamma chain
  • Peptide Ligand Gly-His-Arg-Pro-NH2
KeywordsBLOOD CLOTTING / heterotrimer / protein-peptide complex
Function / homology
Function and homology information


blood coagulation, common pathway / fibrinogen complex / positive regulation of heterotypic cell-cell adhesion / extracellular matrix structural constituent / positive regulation of peptide hormone secretion / protein polymerization / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / fibrinolysis / platelet activation ...blood coagulation, common pathway / fibrinogen complex / positive regulation of heterotypic cell-cell adhesion / extracellular matrix structural constituent / positive regulation of peptide hormone secretion / protein polymerization / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / fibrinolysis / platelet activation / platelet aggregation / positive regulation of ERK1 and ERK2 cascade / signaling receptor binding / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #50 / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #50 / 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
beta-D-mannopyranose / beta-D-galactopyranose / alpha-D-mannopyranose / 2-acetamido-2-deoxy-alpha-D-glucopyranose / Fibrinogen alpha-1 chain / Fibrinogen beta chain / Fibrinogen gamma chain
Similarity search - Component
Biological speciesPetromyzon marinus (sea lamprey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYang, Z. / Spraggon, G. / Pandi, L. / Everse, S.J. / Riley, M. / Doolittle, R.F.
CitationJournal: Biochemistry / Year: 2002
Title: Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide.
Authors: Yang, Z. / Spraggon, G. / Pandi, L. / Everse, S.J. / Riley, M. / Doolittle, R.F.
History
DepositionJun 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 1, 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_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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Oct 27, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / database_PDB_caveat / entity / entity_src_nat / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
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.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_nat.common_name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_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_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 / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num / _struct_ref_seq_dif.seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibrinogen alpha-1 chain
B: Fibrinogen beta chain
C: Fibrinogen gamma chain
D: Fibrinogen alpha-1 chain
E: Fibrinogen beta chain
F: Fibrinogen gamma chain
G: Fibrinogen alpha-1 chain
H: Fibrinogen beta chain
I: Fibrinogen gamma chain
J: Fibrinogen alpha-1 chain
K: Fibrinogen beta chain
L: Fibrinogen gamma chain
M: Peptide Ligand Gly-His-Arg-Pro-NH2
N: Peptide Ligand Gly-His-Arg-Pro-NH2
O: Peptide Ligand Gly-His-Arg-Pro-NH2
P: Peptide Ligand Gly-His-Arg-Pro-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)362,93254
Polymers356,30516
Non-polymers6,62638
Water00
1
A: Fibrinogen alpha-1 chain
B: Fibrinogen beta chain
C: Fibrinogen gamma chain
J: Fibrinogen alpha-1 chain
K: Fibrinogen beta chain
L: Fibrinogen gamma chain
M: Peptide Ligand Gly-His-Arg-Pro-NH2
P: Peptide Ligand Gly-His-Arg-Pro-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,74423
Polymers178,1538
Non-polymers2,59215
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Fibrinogen alpha-1 chain
E: Fibrinogen beta chain
F: Fibrinogen gamma chain
G: Fibrinogen alpha-1 chain
H: Fibrinogen beta chain
I: Fibrinogen gamma chain
N: Peptide Ligand Gly-His-Arg-Pro-NH2
O: Peptide Ligand Gly-His-Arg-Pro-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,18831
Polymers178,1538
Non-polymers4,03523
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.735, 47.654, 244.650
Angle α, β, γ (deg.)88.81, 97.23, 86.17
Int Tables number1
Space group name H-MP1

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Components

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Protein , 3 types, 12 molecules ADGJBEHKCFIL

#1: Protein
Fibrinogen alpha-1 chain


Mass: 14074.052 Da / Num. of mol.: 4 / Fragment: fragment / Source method: isolated from a natural source / Source: (natural) Petromyzon marinus (sea lamprey) / References: UniProt: P02674
#2: Protein
Fibrinogen beta chain


Mass: 37061.211 Da / Num. of mol.: 4 / Fragment: Segment 2 of 2 / Source method: isolated from a natural source / Source: (natural) Petromyzon marinus (sea lamprey) / References: UniProt: P02678
#3: Protein
Fibrinogen gamma chain


Mass: 37475.555 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Petromyzon marinus (sea lamprey) / References: UniProt: P04115

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Protein/peptide / Non-polymers , 2 types, 12 molecules MNOP

#4: Protein/peptide
Peptide Ligand Gly-His-Arg-Pro-NH2


Mass: 465.530 Da / Num. of mol.: 4 / Source method: obtained synthetically
#8: Chemical
ChemComp-CA / CALCIUM ION


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

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Sugars , 6 types, 30 molecules

#5: 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)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#9: 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.: 7
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
#10: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#11: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.75
Details: PEG 3350, MES buffer, pH 6.75, 10 mM CaCl2, VAPOR DIFFUSION, SITTING DROP at 295K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16-8 mg/mllamprey fragment D1drop
250 mMTris1droppH7.0
34 mMGHRPam1drop
45 mM1dropCaCl2
512 %PEG1reservoir
650 mMMES1reservoirpH6.5
720 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Aug 22, 1998
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 74102 / Num. obs: 74102 / % possible obs: 88.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.078
Reflection shellResolution: 2.8→2.87 Å / % possible all: 58.4
Reflection
*PLUS
Num. measured all: 200629
Reflection shell
*PLUS
% possible obs: 58.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 3737 5.05 %RANDOM
Rwork0.245 ---
all0.251 73940 --
obs0.251 73940 87.9 %-
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23934 0 426 0 24360
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.38
Refinement
*PLUS
Highest resolution: 2.8 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.289 / Rfactor Rwork: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS

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