[English] 日本語
Yorodumi
- PDB-3nif: The Closed Headpiece of Integrin IIb 3 and its Complex with an II... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nif
TitleThe Closed Headpiece of Integrin IIb 3 and its Complex with an IIb 3 -Specific Antagonist That Does Not Induce Opening
Components
  • (Monoclonal antibody 10E5 ...) x 2
  • Integrin alphaIIB beta3
  • Integrin beta-3
KeywordsCELL ADHESION/BLOOD CLOTTING / integrin / headpiece / alphaIIB / beta3 / CELL ADHESION-BLOOD CLOTTING complex
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 / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / 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 / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / positive regulation of glomerular mesangial cell proliferation / platelet alpha granule membrane / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / glycinergic synapse / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / positive regulation of vascular endothelial growth factor signaling pathway / : / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / angiogenesis involved in wound healing / filopodium membrane / extracellular matrix binding / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of bone resorption / apolipoprotein A-I-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / positive regulation of leukocyte migration / apoptotic cell clearance / wound healing, spreading of epidermal cells / integrin complex / heterotypic cell-cell adhesion / smooth muscle cell migration / Molecules associated with elastic fibres / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / positive regulation of cell-matrix adhesion / negative chemotaxis / cell adhesion mediated by integrin / cellular response to insulin-like growth factor stimulus / Syndecan interactions / 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 / Integrin cell surface interactions / positive regulation of bone resorption / positive regulation of T cell migration / 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 / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / 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 / VEGFA-VEGFR2 Pathway / platelet aggregation / ruffle membrane / cellular response to mechanical stimulus / positive regulation of fibroblast proliferation / positive regulation of angiogenesis / 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 EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / 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) / 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
Chem-NIF / Integrin beta-3 / Integrin alpha-IIb
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZhu, J.H. / Zhu, J.Q. / Springer, T.A.
CitationJournal: Blood / Year: 2010
Title: Closed headpiece of integrin {alpha}IIb{beta}3 and its complex with an {alpha}IIb{beta}3-specific antagonist that does not induce opening.
Authors: Zhu, J. / Zhu, J. / Negri, A. / Provasi, D. / Filizola, M. / Coller, B.S. / Springer, T.A.
History
DepositionJun 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _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 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrin alphaIIB beta3
B: Integrin beta-3
C: Integrin alphaIIB beta3
D: Integrin beta-3
E: Monoclonal antibody 10E5 heavy chain
F: Monoclonal antibody 10E5 light chain
H: Monoclonal antibody 10E5 heavy chain
L: Monoclonal antibody 10E5 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,30056
Polymers297,1488
Non-polymers6,15348
Water14,232790
1
A: Integrin alphaIIB beta3
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)152,00831
Polymers148,5744
Non-polymers3,43427
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Integrin alphaIIB beta3
D: Integrin beta-3
E: Monoclonal antibody 10E5 heavy chain
F: Monoclonal antibody 10E5 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,29325
Polymers148,5744
Non-polymers2,71921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)259.530, 144.280, 104.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13B
23D
14B
24D
15B
25D
16H
26E
17H
27E
18L
28F
19L
29F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 454
2116C1 - 454
1126B1 - 57
2126D1 - 57
1136B58 - 107
2136D58 - 107
1236B354 - 432
2236D354 - 432
1146B109 - 352
2146D109 - 352
1156B433 - 466
2156D433 - 466
1166H1 - 119
2166E1 - 119
1176H120 - 221
2176E120 - 221
1186L1 - 108
2186F1 - 108
1196L109 - 214
2196F109 - 214

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Integrin alphaIIB beta3 / Platelet membrane glycoprotein IIb / GPalpha IIb / GPIIb / Integrin alpha-IIb heavy chain


Mass: 49515.965 Da / Num. of mol.: 2 / Fragment: Integrin alpha-IIb, residues 32-488
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA2B, GP2B, ITGAB / Plasmid: pCDNA 3.1, pEF1 / Cell (production host): CHO / 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


Mass: 51958.789 Da / Num. of mol.: 2 / Fragment: Integrin beta-3, residues 27-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB3, GP3A / Plasmid: pCDNA 3.1, pEF1 / Cell (production host): CHO / Cell line (production host): Lec 3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P05106

-
Antibody , 2 types, 4 molecules EHFL

#3: Antibody Monoclonal antibody 10E5 heavy chain


Mass: 23766.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell line: 10E5 HYBRIDOMA
#4: Antibody Monoclonal antibody 10E5 light chain


Mass: 23332.686 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell line: 10E5 HYBRIDOMA

-
Sugars , 4 types, 6 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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.: 2
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)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#13: 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

-
Non-polymers , 6 types, 832 molecules

#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-NIF / 2-ethyl-7-piperazin-1-yl-5H-[1,3,4]thiadiazolo[3,2-a]pyrimidin-5-one


Mass: 265.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N5OS
#10: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#12: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 790 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: 11% PEG 8000, 0.2 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.00795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 9, 2008
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00795 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 153422 / Num. obs: 145845 / % possible obs: 95.1 % / Redundancy: 5.53 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 13.3
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.29 / Num. unique all: 11242 / Rsym value: 0.956 / % possible all: 95.6

-
Processing

SoftwareName: REFMAC / Version: 5.5.0093 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NID

3nid


Resolution: 2.4→48.21 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 12.24 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21611 860 0.6 %RANDOM
Rwork0.17563 ---
obs0.17586 144984 95.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2--0.56 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20715 0 361 790 21866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02221632
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214438
X-RAY DIFFRACTIONr_angle_refined_deg1.0921.97429482
X-RAY DIFFRACTIONr_angle_other_deg0.7833.00435111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73752707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24224.355930
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.861153360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.59815112
X-RAY DIFFRACTIONr_chiral_restr0.0670.23256
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02124113
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024268
X-RAY DIFFRACTIONr_mcbond_it1.775513450
X-RAY DIFFRACTIONr_mcbond_other0.36355483
X-RAY DIFFRACTIONr_mcangle_it3.1551021715
X-RAY DIFFRACTIONr_scbond_it4.714108182
X-RAY DIFFRACTIONr_scangle_it6.954207760
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A5861LOOSE POSITIONAL0.285
1A5861LOOSE THERMAL1.9710
2B719LOOSE POSITIONAL0.55
2B719LOOSE THERMAL1.5110
3B1722LOOSE POSITIONAL0.585
3B1722LOOSE THERMAL1.6710
4B3172LOOSE POSITIONAL0.315
4B3172LOOSE THERMAL1.8910
5B418LOOSE POSITIONAL0.45
5B418LOOSE THERMAL2.0110
6H1547LOOSE POSITIONAL0.255
6H1547LOOSE THERMAL1.7210
7H1169LOOSE POSITIONAL0.715
7H1169LOOSE THERMAL1.3210
8L1358LOOSE POSITIONAL0.155
8L1358LOOSE THERMAL1.510
9L1388LOOSE POSITIONAL0.525
9L1388LOOSE THERMAL1.6110
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 52 -
Rwork0.248 10657 -
obs--95.45 %
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)
10.69850.0361-0.13040.90.44880.9404-0.0023-0.0117-0.03150.0938-0.05350.0910.1381-0.11320.05580.190900.05810.0490.0390.142851.22690.14254.113
21.66380.1239-0.36510.646-0.10781.6766-0.0975-0.0692-0.1341-0.10090.0074-0.16030.29830.36130.090.24960.04280.08290.24810.0070.198384.4386.283117.275
310.3731-3.0603-1.16956.0454.265211.4759-0.6074-0.3755-0.08050.89511.2183-1.10121.55723.0399-0.61080.45530.7342-0.11971.8716-0.44220.7883123.55387.5535.034
412.79481.2492-2.48696.9505-0.012315.4708-0.44630.2407-0.9997-0.0988-0.15630.56892.1179-2.33160.60260.5946-0.6710.19760.7888-0.13050.368715.37370.155140.508
53.432-2.0706-2.67514.18174.68877.5951-0.0737-0.22250.30820.16520.5313-0.2970.35131.0364-0.45760.06810.0729-0.03270.4452-0.14340.469101.389106.77552.359
61.9990.6139-1.59661.7327-2.650410.3972-0.23580.503-0.068-0.09510.1248-0.01870.5584-0.9650.1110.1379-0.19170.01530.52280.02350.141331.59787.123115.911
70.70520.34940.01511.92650.66160.9069-0.0028-0.06570.12730.0280.0801-0.1106-0.11830.0677-0.07730.2170.01490.05550.04670.00650.17668.083118.01263.278
81.7392-0.06210.29470.5276-0.37692.0621-0.04340.21460.3086-0.07910.05440.0053-0.1415-0.226-0.0110.2943-0.02910.04360.27820.07530.189660.91102.05599.433
98.17280.9668-1.9153.92520.627818.33330.1899-0.0441-0.0014-0.77420.3925-0.50880.06571.932-0.58230.23170.2420.11721.1078-0.02320.5957116.188.33619.24
1013.87552.6832-2.24094.27786.757913.924-0.0862-0.1120.18510.1933-0.41130.21710.3501-1.39290.49750.2025-0.18740.13370.6016-0.13370.305420.85779.825154.007
113.7262-0.3259-1.07923.8540.29743.61060.0569-0.63860.01320.9802-0.06330.1670.1903-0.20690.00630.3576-0.08860.14970.4697-0.07690.259118.2196.56882.383
123.9508-2.5380.3223.188-0.76164.15420.26210.6651-0.0716-1.1959-0.3253-0.31191.34250.23540.06321.0103-0.00880.37510.7739-0.01930.3927115.35189.88286.092
138.89543.19031.70884.57770.89099.3469-0.2038-0.32-2.0230.43520.0880.08131.42240.29980.11570.36650.16830.35490.30930.21.3944-14.43681.36893.076
149.0372.57454.06490.67762.21026.92960.86341.4336-0.96850.05530.082-0.80981.52121.0217-0.94541.56490.99690.28371.64410.20651.5929151.8882.53179.374
155.10231.1514-0.25374.06941.22191.9232-0.00670.1941-0.0634-0.017-0.44680.9709-0.009-0.75420.45360.08140.00160.09910.5839-0.19490.47776.73695.41864.418
166.2869-0.88590.82234.1516-1.52183.0607-0.0889-0.21640.7616-0.0544-0.3243-1.17990.1730.71980.41320.2234-0.05010.22560.77240.05440.7505125.999.443102.048
176.7108-1.1515-2.96592.63081.96438.718-0.5240.4875-1.53860.2439-0.17030.58710.0315-0.38640.69430.0883-0.04640.17710.4014-0.05410.9814-22.25893.35986.288
180.9186-0.8374-0.19163.24152.298610.17420.01380.25690.1747-1.2355-0.1724-0.6767-0.46761.99890.15860.95850.130.53281.7260.50261.4861154.59198.20180.007
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 454
2X-RAY DIFFRACTION1A1 - 455
3X-RAY DIFFRACTION2C1 - 453
4X-RAY DIFFRACTION2C2 - 455
5X-RAY DIFFRACTION3B1 - 57
6X-RAY DIFFRACTION4D1 - 57
7X-RAY DIFFRACTION5B58 - 107
8X-RAY DIFFRACTION5B354 - 432
9X-RAY DIFFRACTION6D58 - 107
10X-RAY DIFFRACTION6D354 - 432
11X-RAY DIFFRACTION7B109 - 352
12X-RAY DIFFRACTION8D109 - 352
13X-RAY DIFFRACTION9B433 - 466
14X-RAY DIFFRACTION10D433 - 466
15X-RAY DIFFRACTION11H1 - 119
16X-RAY DIFFRACTION12E1 - 119
17X-RAY DIFFRACTION13H120 - 221
18X-RAY DIFFRACTION14E120 - 221
19X-RAY DIFFRACTION15L1 - 108
20X-RAY DIFFRACTION16F1 - 108
21X-RAY DIFFRACTION17L109 - 214
22X-RAY DIFFRACTION18F109 - 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