[English] 日本語
Yorodumi
- PDB-2vdo: Integrin AlphaIIbBeta3 Headpiece Bound to Fibrinogen Gamma chain ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vdo
TitleIntegrin AlphaIIbBeta3 Headpiece Bound to Fibrinogen Gamma chain peptide, HHLGGAKQAGDV
Components
  • (MONOCLONAL ANTIBODY 10E5 ...) x 2
  • FIBRINOGEN, GAMMA POLYPEPTIDE
  • INTEGRIN ALPHA-IIB
  • INTEGRIN BETA-3
KeywordsCELL ADHESION/IMMUNE SYSTEM / CELL ADHESION-IMMUNE SYSTEM COMPLEX / FIBRINOGEN BINDING / PLATELET INTEGRIN ALPHAIIBBETA3 / GLYCOPROTEIN / CELL ADHESION / MEMBRANE / INTEGRIN / RECEPTOR / ANTAGONIST / HOST-VIRUS INTERACTION / PYRROLIDONE CARBOXYLIC ACID / TRANSMEMBRANE / PHOSPHORYLATION / DISEASE MUTATION / CLEAVAGE ON PAIR OF BASIC RESIDUES
Function / homology
Function and homology information


fibrinogen complex / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / alpha9-beta1 integrin-ADAM8 complex / response to platelet-derived growth factor / integrin alphaIIb-beta3 complex / blood coagulation, fibrin clot formation / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure ...fibrinogen complex / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / alpha9-beta1 integrin-ADAM8 complex / response to platelet-derived growth factor / integrin alphaIIb-beta3 complex / blood coagulation, fibrin clot formation / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / platelet alpha granule membrane / Regulation of TLR by endogenous ligand / positive regulation of glomerular mesangial cell proliferation / platelet alpha granule / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / smooth muscle cell migration / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / positive regulation of leukocyte migration / alphav-beta3 integrin-HMGB1 complex / negative regulation of lipid transport / vascular endothelial growth factor receptor 2 binding / angiogenesis involved in wound healing / positive regulation of vascular endothelial growth factor signaling pathway / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / positive regulation of bone resorption / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / cell-cell adhesion mediated by integrin / filopodium membrane / extracellular matrix binding / MyD88 deficiency (TLR2/4) / glycinergic synapse / positive regulation of fibroblast migration / positive regulation of cell adhesion mediated by integrin / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of heterotypic cell-cell adhesion / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / negative regulation of low-density lipoprotein particle clearance / apoptotic cell clearance / wound healing, spreading of epidermal cells / positive regulation of smooth muscle cell migration / integrin complex / Molecules associated with elastic fibres / heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / cell adhesion mediated by integrin / plasminogen activation / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / negative chemotaxis / positive regulation of osteoblast proliferation / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / cellular response to insulin-like growth factor stimulus / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / regulation of postsynaptic neurotransmitter receptor internalization / extracellular matrix structural constituent / positive regulation of peptide hormone secretion / cell-substrate adhesion / protein disulfide isomerase activity / microvillus membrane / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / protein secretion / negative regulation of endothelial cell apoptotic process / TGF-beta receptor signaling activates SMADs / lamellipodium membrane / fibronectin binding / positive regulation of exocytosis / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of vasoconstriction / Integrin cell surface interactions / positive regulation of substrate adhesion-dependent cell spreading / ECM proteoglycans / : / substrate adhesion-dependent cell spreading / positive regulation of T cell migration / protein polymerization / fibrinolysis / cell-matrix adhesion / embryo implantation / coreceptor activity / Integrin signaling / positive regulation of endothelial cell proliferation / positive regulation of smooth muscle cell proliferation / positive regulation of endothelial cell migration / cell adhesion molecule binding / platelet alpha granule lumen / integrin-mediated signaling pathway / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / response to activity / protein kinase C binding / positive regulation of protein secretion
Similarity search - Function
ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / ligand-binding face of the semaphorins, domain 2 / Integrin alpha, N-terminal / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. ...ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / ligand-binding face of the semaphorins, domain 2 / Integrin alpha, N-terminal / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / 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. / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / : / Integrin beta tail domain / Integrin beta cytoplasmic domain / Integrin alpha Ig-like domain 3 / Integrin_b_cyt / : / Integrin EGF domain / EGF-like domain, extracellular / EGF-like domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin alpha cytoplasmic region / : / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / PSI domain / domain found in Plexins, Semaphorins and Integrins / EGF-like domain signature 1. / 7 Propeller / Methylamine Dehydrogenase; Chain H / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Fibrinogen gamma chain / Integrin beta-3 / Integrin alpha-IIb / Fibrinogen gamma chain
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.51 Å
AuthorsSpringer, T.A. / Zhu, J. / Xiao, T.
Citation
Journal: J.Cell Biol. / Year: 2008
Title: Structural Basis for Distinctive Recognition of Fibrinogen Gammac Peptide by the Platelet Integrin Alphaiibbeta3.
Authors: Springer, T.A. / Zhu, J. / Xiao, T.
#1: Journal: Nature / Year: 2004
Title: Structural Basis for Allostery in Integrins and Binding to Fibrinogen-Mimetic Therapeutics
Authors: Xiao, T. / Takagi, J. / Coller, B.S. / Wang, J.-H. / Springer, T.A.
History
DepositionOct 10, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_conn_type / 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_database_status.status_code_sf / _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.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.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: INTEGRIN ALPHA-IIB
B: INTEGRIN BETA-3
C: FIBRINOGEN, GAMMA POLYPEPTIDE
H: MONOCLONAL ANTIBODY 10E5 HEAVY CHAIN
L: MONOCLONAL ANTIBODY 10E5 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,55019
Polymers148,2915
Non-polymers3,25914
Water18,7901043
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11960 Å2
ΔGint-75.9 kcal/mol
Surface area72750 Å2
MethodPQS
Unit cell
Length a, b, c (Å)148.331, 148.331, 176.567
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein INTEGRIN ALPHA-IIB / PLATELET MEMBRANE GLYCOPROTEIN IIB / GPALPHA IIB / GPIIB / INTEGRIN ALPHA-IIB HEAVY CHAIN


Mass: 49030.367 Da / Num. of mol.: 1 / Fragment: HEADPIECE, RESIDUES 32-483
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): LEC 3.2.8.1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P08514
#2: Protein INTEGRIN BETA-3 / PLATELET MEMBRANE GLYCOPROTEIN IIIA / GPIIIA / CD61 ANTIGEN


Mass: 50969.664 Da / Num. of mol.: 1 / Fragment: HEADPIECE, RESIDUES 27-487
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): LEC 3.2.8.1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P05106

-
Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide FIBRINOGEN, GAMMA POLYPEPTIDE


Mass: 1192.305 Da / Num. of mol.: 1 / Fragment: GAMMA CHAIN C-TERMINAL PEPTIDE, RESIDUES 426-437 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q53Y18, UniProt: P02679*PLUS

-
Antibody , 2 types, 2 molecules HL

#4: Antibody MONOCLONAL ANTIBODY 10E5 HEAVY CHAIN


Mass: 23766.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: 10E5 HYBRIDOMA / Strain: BALB/C
#5: Antibody MONOCLONAL ANTIBODY 10E5 LIGHT CHAIN


Mass: 23332.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: 10E5 HYBRIDOMA / Strain: BALB/C

-
Sugars , 3 types, 5 molecules

#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 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]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{}}}}}}LINUCSPDB-CARE
#10: 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.: 3
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

-
Non-polymers , 4 types, 1052 molecules

#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#11: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1043 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsACCORDING TO THE AUTHORS THE CORRECT CHAIN A SEQUENCE IS ANNOTATED IN NCBI ENTRY GI 88758615 WHICH ...ACCORDING TO THE AUTHORS THE CORRECT CHAIN A SEQUENCE IS ANNOTATED IN NCBI ENTRY GI 88758615 WHICH SHOULD BE USED IN PLACE OF P08514. ACCORDING TO THE AUTHORS THE CORRECT CHAIN C SEQUENCE IS ANNOTATED IN NCBI ENTRY GI 70906437 WHICH CORRESPONDS TO THE UNIPROT ENTRY Q53Y18

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.2 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 11% PEG 3350, 0.7 M MAGNESIUM ACETATE, 0.1 M SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.07223
DetectorType: CUSTOM (SBC2 3K) / Detector: CCD / Date: Dec 15, 2004 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07223 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 557015 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.2
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.8 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.51→46.13 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.948 / SU B: 10.761 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 3807 5.1 %RANDOM
Rwork0.148 ---
obs0.15 71126 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.02 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.51→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10369 0 205 1043 11617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02211034
X-RAY DIFFRACTIONr_bond_other_d0.0010.027394
X-RAY DIFFRACTIONr_angle_refined_deg1.0461.97915073
X-RAY DIFFRACTIONr_angle_other_deg0.7893.00318001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.49751397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.58824.324481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.148151735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8921561
X-RAY DIFFRACTIONr_chiral_restr0.0650.21698
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212310
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022178
X-RAY DIFFRACTIONr_nbd_refined0.1830.21982
X-RAY DIFFRACTIONr_nbd_other0.1790.27585
X-RAY DIFFRACTIONr_nbtor_refined0.1720.25314
X-RAY DIFFRACTIONr_nbtor_other0.0810.25775
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2868
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1030.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1770.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.85257079
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.8761011024
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.93954606
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.908104028
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.51→2.57 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.289 260
Rwork0.216 4785
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)
14.339-2.4833-0.628613.42160.00993.7125-0.1973-0.0949-0.34190.5329-0.1952-0.94660.55440.83230.3925-0.18820.0713-0.05530.09930.40040.0165132.93212.10278.357
23.17710.0302-0.14086.14051.753.33150.0547-0.0095-0.1112-0.1423-0.283-0.53690.10760.36260.2283-0.24840.03130.0143-0.06290.2485-0.0864129.01721.61568.924
31.0076-0.4411-0.35261.6247-0.6232.10370.0394-0.01310.00860.2021-0.2131-0.2712-0.05830.38530.1737-0.2743-0.0931-0.0503-0.11510.1361-0.1125118.53533.37164.289
42.87860.4195-1.9371.4552-0.11622.5665-0.01990.0112-0.1160.0517-0.13450.20480.0121-0.04210.1545-0.2434-0.0866-0.0376-0.16510.0904-0.1988106.97335.90363.494
50.9301-0.0965-0.6960.9556-0.48771.90820.02720.134-0.14510.062-0.1453-0.01070.2669-0.12520.1181-0.1889-0.0824-0.01-0.18440.0621-0.1462105.94324.31163.811
62.46510.0965-0.32522.19190.54473.8818-0.05580.1083-0.2652-0.0325-0.19120.13920.4367-0.28240.247-0.0511-0.13860.0535-0.27040.052-0.090399.55612.95572.219
73.1282-0.3323-0.81895.38292.95014.2387-0.1844-0.2593-0.41080.5516-0.04530.18280.99450.01430.22970.0178-0.09210.1011-0.2870.2083-0.0417107.6087.04284.245
83.10180.4561-0.06683.31611.56373.5102-0.156-0.051-0.4472-0.0115-0.3381-0.05980.7308-0.07410.49410.1302-0.03690.1245-0.29590.1794-0.0399110.1112.66378.407
92.99890.7461-0.50033.14860.0213.0821-0.1362-0.2629-0.44310.2734-0.2923-0.38810.5990.62620.4285-0.04880.10290.0088-0.10370.30950.0185124.1767.32879.987
106.1423-1.88395.52954.0518-2.933412.2091-0.2719-0.7559-0.15861.19340.3932-0.4537-1.3284-1.1794-0.12130.44460.2057-0.1188-0.3282-0.0935-0.3172106.26821.349169.156
119.6249-4.320318.110210.998-15.105639.4491-0.8897-0.17580.73671.18940.2821-0.3446-3.5011-1.13160.60770.63420.24070.0477-0.0747-0.0627-0.0889103.37729.314150.342
120.29-0.36390.10690.6087-0.60011.4657-0.0295-0.16660.02780.40450.027-0.0117-0.43640.09480.00250.1489-0.220.0447-0.08050.0203-0.142197.2738.152104.239
131.4144-0.2922-0.74881.58020.12982.14190.0546-0.2660.09580.4302-0.099-0.1348-0.06020.22470.0444-0.0421-0.1953-0.0108-0.15830.0529-0.1993102.76634.21895.967
143.7877-2.79089.7732.6048-6.484426.15090.68590.6576-0.4734-0.34280.19390.16211.41970.8471-0.87980.249-0.10480.0497-0.1016-0.0054-0.123499.94222.651130.871
156.1854-1.47698.9392.3089-1.780223.1613-0.45990.61060.190.62330.4505-0.6388-2.29811.68940.00940.4274-0.103-0.0343-0.3109-0.0266-0.1764109.15328.251149.069
163.76464.5045-6.97585.4692-8.989618.1237-0.2075-0.84781.08232.1226-0.1486-1.9113-4.32273.7870.35611.9511-0.1471-0.86580.8137-0.18890.6802119.08731.335183.163
1712.0138-12.16868.831317.6137-9.629311.88230.35070.3005-1.1269-0.78070.13890.80240.9651-0.1217-0.4896-0.2245-0.17-0.0138-0.06960.0502-0.090289.76936.53533.167
182.84150.26940.3731.8079-0.04862.12040.01170.010.0240.01310.03210.15620.2438-0.2276-0.0438-0.2765-0.049-0.0106-0.10440.086-0.141593.9441.84741.179
193.2994-0.66811.2150.4697-0.87492.9323-0.06180.02110.0989-0.02390.00140.02340.1811-0.31980.0604-0.2598-0.0739-0.0109-0.10330.0807-0.113793.75542.71643.4
201.2362-1.13280.21211.09570.26793.74950.2808-0.0405-0.2693-0.016-0.15280.0973-0.0467-0.6355-0.1279-0.3169-0.074-0.07940.11950.047-0.073286.19947.56512.7
217.9266-2.4433-4.77391.00041.604114.29860.45140.2063-0.7114-0.2674-0.38410.12430.7970.2007-0.0672-0.29320.0717-0.115-0.1692-0.0104-0.207892.27644.624.669
2210.616-0.458-3.79961.9983-0.203513.2310.432-0.42390.002-0.3732-0.1038-0.04660.60020.6535-0.3282-0.32570.1107-0.0909-0.19870.0562-0.278894.30147.3979.179
237.77570.4237-2.45233.9136-0.97586.24470.61180.4813-1.2766-0.854-0.7092-0.03820.58310.39610.09740.1870.2758-0.096-0.0426-0.1315-0.147693.77840.43-3.658
246.97622.5961-8.48354.6661-0.070415.777-0.3870.5271-0.6436-1.33350.12290.84091.9895-0.80190.2641-0.18550.0578-0.27590.0345-0.0964-0.095685.83743.55-1.931
252.01340.736-0.57590.75620.41192.10070.1040.27830.2746-0.0646-0.04110.0119-0.06640.0992-0.063-0.27260.0350.017-0.09490.1437-0.0562114.10749.94935.129
264.53450.3649-0.06691.8099-0.83682.2669-0.01570.3718-0.2639-0.15990.133-0.07110.53190.1353-0.1174-0.21370.0267-0.0125-0.11330.0945-0.1353113.40139.00836.169
273.9213-0.7525-1.76550.95420.05165.4599-0.02170.3695-0.051-0.0058-0.05390.11470.3861-0.14190.0755-0.2667-0.0084-0.0302-0.1490.0966-0.1319112.18145.5635.638
282.2854-1.93743.52351.9437-2.61315.89580.46210.3527-0.2704-0.2924-0.34350.13540.48350.3681-0.1186-0.28810.06220.0160.04650.059-0.1507100.30552.9538.076
296.6961-4.46022.97535.2547-2.35222.8572-0.1208-0.19720.50440.1206-0.1868-0.4294-0.06630.32980.3076-0.38340.051-0.00310.14930.0308-0.244101.45959.6278.724
309.7968-5.05964.53064.3387-2.68584.71330.05110.27580.0881-0.2341-0.1424-0.0250.03750.27840.0913-0.35120.0468-0.0067-0.00060.0134-0.258595.18859.8362.973
3114.1961-4.62429.73125.2787-5.305912.64410.53711.52110.3215-0.515-0.7958-0.39580.26651.29390.2587-0.3440.16220.09010.17090.144-0.1917102.6662.279-2.398
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 17
2X-RAY DIFFRACTION2A18 - 62
3X-RAY DIFFRACTION3A63 - 115
4X-RAY DIFFRACTION4A116 - 167
5X-RAY DIFFRACTION5A168 - 243
6X-RAY DIFFRACTION6A244 - 290
7X-RAY DIFFRACTION7A291 - 326
8X-RAY DIFFRACTION8A327 - 372
9X-RAY DIFFRACTION9A373 - 452
10X-RAY DIFFRACTION10B1 - 72
11X-RAY DIFFRACTION11B79 - 98
12X-RAY DIFFRACTION12B99 - 172
13X-RAY DIFFRACTION13B173 - 338
14X-RAY DIFFRACTION14B339 - 393
15X-RAY DIFFRACTION15B394 - 437
16X-RAY DIFFRACTION16B438 - 461
17X-RAY DIFFRACTION17H1 - 13
18X-RAY DIFFRACTION18H14 - 54
19X-RAY DIFFRACTION19H55 - 110
20X-RAY DIFFRACTION20H111 - 134
21X-RAY DIFFRACTION21H137 - 164
22X-RAY DIFFRACTION22H165 - 189
23X-RAY DIFFRACTION23H190 - 206
24X-RAY DIFFRACTION24H207 - 221
25X-RAY DIFFRACTION25L1 - 38
26X-RAY DIFFRACTION26L39 - 69
27X-RAY DIFFRACTION27L70 - 97
28X-RAY DIFFRACTION28L98 - 135
29X-RAY DIFFRACTION29L136 - 167
30X-RAY DIFFRACTION30L168 - 197
31X-RAY DIFFRACTION31L198 - 214

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more