[English] 日本語
Yorodumi
- PDB-2vdm: Re-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antago... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vdm
TitleRe-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antagonist Tirofiban
Components
  • (MONOCLONAL ANTIBODY 10E5 ...) x 2
  • 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


tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / maintenance of postsynaptic specialization structure / regulation of extracellular matrix organization ...tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / maintenance of postsynaptic specialization structure / regulation of extracellular matrix organization / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / glycinergic synapse / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / : / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / angiogenesis involved in wound healing / platelet-derived growth factor receptor binding / alphav-beta3 integrin-IGF-1-IGF1R complex / filopodium membrane / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of fibroblast migration / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / positive regulation of cell adhesion mediated by integrin / positive regulation of leukocyte migration / apoptotic cell clearance / activation of protein kinase activity / wound healing, spreading of epidermal cells / integrin complex / heterotypic cell-cell adhesion / Molecules associated with elastic fibres / smooth muscle cell migration / positive regulation of cell-matrix adhesion / cell adhesion mediated by integrin / negative chemotaxis / Syndecan interactions / cellular response to insulin-like growth factor stimulus / microvillus membrane / p130Cas linkage to MAPK signaling for integrins / positive regulation of smooth muscle cell migration / regulation of postsynaptic neurotransmitter receptor internalization / protein disulfide isomerase activity / cell-substrate adhesion / positive regulation of osteoblast proliferation / PECAM1 interactions / TGF-beta receptor signaling activates SMADs / GRB2:SOS provides linkage to MAPK signaling for Integrins / lamellipodium membrane / platelet-derived growth factor receptor signaling pathway / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ECM proteoglycans / positive regulation of bone resorption / positive regulation of T cell migration / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / coreceptor activity / cell adhesion molecule binding / cellular response to platelet-derived growth factor stimulus / positive regulation of endothelial cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / Integrin signaling / embryo implantation / substrate adhesion-dependent cell spreading / protein kinase C binding / cell-matrix adhesion / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Signal transduction by L1 / response to activity / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / positive regulation of smooth muscle cell proliferation / wound healing / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / cell-cell adhesion / platelet activation / platelet aggregation / VEGFA-VEGFR2 Pathway / ruffle membrane / cellular response to mechanical stimulus / positive regulation of fibroblast proliferation / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / Signaling by RAF1 mutants
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 / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain ...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 / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / : / Integrin alpha Ig-like domain 3 / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrins beta chain EGF (I-EGF) domain profile. / Integrin alpha cytoplasmic region / 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) / EGF-like domain, extracellular / EGF-like domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / 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 / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TIROFIBAN / Integrin beta-3 / Integrin alpha-IIb
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
SupersessionSep 2, 2008ID: 1TY5
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 1.4Nov 20, 2019Group: Advisory / Derived calculations / Other
Category: database_PDB_caveat / pdbx_database_status ...database_PDB_caveat / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_database_status.status_code_sf
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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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
H: MONOCLONAL ANTIBODY 10E5 HEAVY CHAIN
L: MONOCLONAL ANTIBODY 10E5 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,79819
Polymers147,0994
Non-polymers3,69915
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10970 Å2
ΔGint-70.7 kcal/mol
Surface area71810 Å2
MethodPQS
Unit cell
Length a, b, c (Å)148.577, 148.577, 177.239
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

-
Antibody , 2 types, 2 molecules HL

#3: 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
#4: 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

#5: 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)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#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.: 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 , 5 types, 365 molecules

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


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


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#10: Chemical ChemComp-AGG / TIROFIBAN / N-(BUTYLSULFONYL)-O-[4-(4-PIPERIDINYL)BUTYL]-L-TYROSINE


Mass: 440.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H36N2O5S / Comment: medication, inhibitor*YM
#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.: 355 / 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.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.5 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10-12% PEG3350, 0.7 M MAGNESIUM ACETATE, 0.1 M IMIDAZOLE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976
DetectorType: CUSTOM (SBC2 3K) / Detector: CCD / Date: Oct 4, 2003 / Details: MIRROR
RadiationMonochromator: RH-COATED SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 50516 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 6 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TXV

1txv
PDB Unreleased entry


Resolution: 2.9→46.23 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 21.955 / SU ML: 0.213 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.958 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THESE ARE RE-REFINED COORDINATES OF THE PREVIOUS WWPDB SUBMISSION 1TY5. THE STARTING MODEL WAS A 2.4 ANGSTROM STRUCTURE WITH A DIFFERENT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THESE ARE RE-REFINED COORDINATES OF THE PREVIOUS WWPDB SUBMISSION 1TY5. THE STARTING MODEL WAS A 2.4 ANGSTROM STRUCTURE WITH A DIFFERENT BOUND LIGAND. THE MODEL IS REFINED TO LOWER RFREE. ONE SEQUENCE MISTAKE IN THE AIIB SUBUNIT IS CORRECTED. MORE OF BETA SUBUNIT DOMAIN I-EGF1 IS BUILT. THE ARRANGEMENT OF ATOMS AT CENTERS IN THE LIGAND THAT ARE FREE TO REARRANGE IN SOLVENT IS CHANGED. MISTAKES IN CARBOHYDRATE ANOMERIC LINKAGES ARE ALSO CORRECTED.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 2464 5 %RANDOM
Rwork0.167 ---
obs0.169 46776 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20.6 Å20 Å2
2--1.21 Å20 Å2
3----1.81 Å2
Refinement stepCycle: LAST / Resolution: 2.9→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10291 0 235 355 10881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02210871
X-RAY DIFFRACTIONr_bond_other_d0.0010.027295
X-RAY DIFFRACTIONr_angle_refined_deg0.9251.98114826
X-RAY DIFFRACTIONr_angle_other_deg0.7593.00517675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.26751353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66524.307469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.839151688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9041559
X-RAY DIFFRACTIONr_chiral_restr0.0570.21666
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212068
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022138
X-RAY DIFFRACTIONr_nbd_refined0.180.22008
X-RAY DIFFRACTIONr_nbd_other0.1690.27548
X-RAY DIFFRACTIONr_nbtor_refined0.170.25311
X-RAY DIFFRACTIONr_nbtor_other0.080.25649
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2453
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0990.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1480.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.24456968
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0561010842
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.15454547
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.907103979
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: 2.9→2.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.333 154
Rwork0.271 3089
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)
17.9623-3.37841.02826.1541-1.7572.9042-0.20170.0139-0.67610.8316-0.2202-1.43990.55050.89260.4220.04260.17130.03260.17420.38860.0229133.16412.35978.515
23.18531.43970.43014.9013-0.86451.5567-0.08130.0068-0.2166-0.0961-0.164-0.45280.39960.42120.2453-0.14610.05850.03790.10270.2725-0.1593129.18321.89569.137
30.2918-0.3883-0.50442.4491-0.6761.8113-0.0771-0.0585-0.04520.2667-0.1352-0.44120.03080.47160.2123-0.202-0.0562-0.0519-0.09170.153-0.208118.68433.64164.57
44.6967-0.7261-1.70641.9635-0.28382.73610.05490.1301-0.26870.1513-0.32740.10880.107-0.05940.2725-0.1657-0.0891-0.0587-0.13980.0761-0.3337107.0436.11263.922
50.9343-0.0784-0.71691.7002-1.04322.34630.00410.1575-0.2321-0.0494-0.13960.00290.2176-0.14010.1355-0.1738-0.04370.0008-0.18850.0543-0.2559106.124.49864.159
62.75-0.5960.08492.09470.43583.75550.0990.1378-0.4223-0.0801-0.093-0.03590.4405-0.0801-0.006-0.0049-0.13480.0662-0.23170.083-0.168599.82313.06772.55
73.3487-0.6427-1.42626.09474.52426.8095-0.2663-0.3986-0.51380.4917-0.03070.10570.68010.14950.2970.092-0.02120.0797-0.16660.2129-0.1034107.9167.21284.58
81.7385-0.9384-1.19974.32351.33424.8754-0.1540.0756-0.3235-0.088-0.25330.04020.8708-0.12050.40730.2035-0.01450.093-0.17320.2434-0.0876110.6192.94178.913
92.6329-0.1035-0.72193.3332-0.05632.7348-0.129-0.1483-0.44860.0701-0.2113-0.31820.61290.46120.34030.09320.13230.05180.00630.3060.0159124.457.52980.221
103.4228-2.10582.9564.4598-3.60538.5569-0.2967-0.61810.0381.42060.4282-0.2532-1.0628-0.9177-0.13151.03330.0899-0.19580.142-0.13540.0702106.53421.28169.667
1110.9463-5.446519.46689.0368-17.104943.319-0.5629-0.88260.52691.19360.3049-0.5801-2.3939-2.25720.25810.7990.16270.02430.0967-0.01280.0161103.33929.827150.169
120.2053-0.31040.21470.7393-1.17872.92550.014-0.3212-0.05860.5553-0.03010.1005-0.61810.07810.01610.197-0.2150.0066-0.00670.0271-0.216897.60338.251104.601
131.9689-0.5951-1.03071.26320.2152.24140.0106-0.3510.07740.4131-0.0953-0.1755-0.14180.20270.08470.0199-0.151-0.0181-0.07690.0714-0.2783103.09234.34696.32
142.7377-2.02588.01712.7689-5.785423.49410.67790.5086-0.87120.00080.3372-0.181.29130.5944-1.01520.326-0.04470.05390.16930.02490.0074100.33322.626131.302
153.1437-1.45814.32352.0877-2.694413.2447-0.29740.45870.16750.77840.4134-0.7168-1.68231.2319-0.1160.7095-0.0481-0.1040.10610.00060.1305109.47228.127149.717
16000000-0.3907-1.4030.1351-0.14350.3542-0.333-1.22213.13130.03662.3534-0.1422-1.03681.13380.02851.0922119.25131.176183.81
178.1816-10.71087.965117.3548-11.793315.60830.59470.5126-0.5792-0.9268-0.67160.09081.3108-0.01660.0769-0.1793-0.23550.006-0.07750.0225-0.230789.7136.75633.538
184.0201-0.67231.60120.5460.58852.42720.0598-0.02410.09180.01040.04960.24280.3504-0.2838-0.1094-0.2707-0.0586-0.0066-0.18260.0412-0.283893.9542.17441.469
192.3041-0.58221.87020.323-1.04383.3734-0.08520.06870.1227-0.02810.0130.04790.1463-0.32660.0722-0.251-0.05540.0136-0.11510.0647-0.251293.7542.97543.755
202.5317-1.6794-0.34641.42371.23853.33230.32460.322-0.2627-0.3160.07360.3332-0.4413-0.771-0.3982-0.2031-0.1126-0.0713-0.00780.0045-0.124786.12347.60413.23
219.70510.0259-6.44472.41211.227613.02630.14410.5591-0.1245-0.37150.1636-0.2931.1826-0.0728-0.30770.00540.1119-0.16510.05080.0214-0.068392.09144.5375.211
226.00811.9584-0.30671.2575-3.415317.76810.2738-0.00170.3364-0.5594-0.29280.18530.25440.71850.019-0.04710.0869-0.0635-0.10980.0474-0.182994.25547.4119.484
2311.28330.1457-4.81462.65811.71053.23750.31970.0149-1.3704-0.9467-0.5993-0.20130.41621.21920.27970.52560.28910.02610.2778-0.0733-0.023893.65540.46-3.368
2411.99144.4986-14.49846.2193-3.850922.8893-0.09240.65050.2201-1.24020.50471.16321.5531-1.0156-0.41230.0462-0.0228-0.18060.3491-0.0857-0.03585.71543.671-1.723
250.5417-0.0735-0.48650.930.21950.89880.08850.22930.0792-0.1718-0.0168-0.0873-0.31250.0307-0.0718-0.22150.01190.0297-0.09650.1222-0.1972114.11650.12235.445
263.55221.5928-2.02172.9398-1.82662.67910.11470.4019-0.4701-0.18580.0051-0.19380.51920.1627-0.1198-0.2520.06950.0014-0.16280.0119-0.2684113.39139.15436.469
274.12830.8981-2.05880.6033-1.35233.0316-0.08830.2990.0348-0.03270.0652-0.03410.37720.1340.0232-0.23880.0128-0.0384-0.16020.0771-0.2579112.15645.73435.936
280.766-1.50091.35472.9411-2.67275.21730.52950.2929-0.1838-0.4829-0.30740.15870.66460.2299-0.2221-0.19530.02510.00470.13940.0856-0.2383100.25253.0358.427
296.3505-3.13313.07045.3999-2.80944.6282-0.0607-0.22930.46130.3239-0.1691-0.1658-0.05450.28020.2298-0.23810.0085-0.00860.18790.0154-0.2675101.45159.6559.063
308.2964-4.49093.95963.7263-1.23374.83360.01540.2544-0.039-0.488-0.0491-0.12070.01830.20250.0337-0.2355-0.0190.05130.08840.0518-0.212795.0759.9323.196
3113.3494-8.15495.99177.9082-6.52889.22640.16421.6823-1.0121-0.5470.05350.1836-0.3751.0167-0.2176-0.07460.08680.11830.1750.1123-0.1636102.8962.3-1.874
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 DIFFRACTION11B78 - 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