[English] 日本語
Yorodumi
- PDB-4oga: Insulin in complex with Site 1 of the human insulin receptor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4oga
TitleInsulin in complex with Site 1 of the human insulin receptor
Components
  • (Insulin receptor ...) x 2
  • (monoclonal antibody fab 83-7 fragment - ...) x 2
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE RECEPTOR/HORMONE/IMMUNE SYSTEM / CELL SURFACE RECEPTOR/IMMUNE SYSTEM / INSULIN RECEPTOR / CT PEPTIDE / INSULIN / HORMONE RECEPTOR-HORMONE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


regulation of female gonad development / positive regulation of meiotic cell cycle / positive regulation of developmental growth / insulin-like growth factor II binding / male sex determination / exocrine pancreas development / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / positive regulation of protein-containing complex disassembly ...regulation of female gonad development / positive regulation of meiotic cell cycle / positive regulation of developmental growth / insulin-like growth factor II binding / male sex determination / exocrine pancreas development / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / positive regulation of protein-containing complex disassembly / cargo receptor activity / dendritic spine maintenance / PTB domain binding / insulin binding / negative regulation of NAD(P)H oxidase activity / neuronal cell body membrane / adrenal gland development / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / negative regulation of fatty acid metabolic process / nitric oxide-cGMP-mediated signaling / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / amyloid-beta clearance / positive regulation of peptide hormone secretion / activation of protein kinase activity / Regulation of gene expression in beta cells / positive regulation of respiratory burst / regulation of embryonic development / transport across blood-brain barrier / positive regulation of receptor internalization / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / insulin receptor substrate binding / negative regulation of protein secretion / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / epidermis development / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / regulation of protein localization to plasma membrane / positive regulation of nitric oxide mediated signal transduction / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / phosphatidylinositol 3-kinase binding / heart morphogenesis / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / transport vesicle / positive regulation of protein autophosphorylation / dendrite membrane / insulin-like growth factor receptor binding / Insulin receptor recycling / receptor-mediated endocytosis / positive regulation of protein metabolic process / NPAS4 regulates expression of target genes / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / learning / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / caveola / endosome lumen / positive regulation of cytokine production / acute-phase response / regulation of transmembrane transporter activity / positive regulation of protein secretion / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / positive regulation of MAP kinase activity / memory / insulin receptor binding / cognition / negative regulation of protein catabolic process / receptor internalization / positive regulation of neuron projection development / hormone activity / receptor protein-tyrosine kinase / vasodilation / Golgi lumen / cellular response to growth factor stimulus / positive regulation of protein localization to nucleus
Similarity search - Function
24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Alpha-Beta Horseshoe ...24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Alpha-Beta Horseshoe / Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Ribbon / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Insulin / Insulin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsLawrence, M.C. / Menting, J.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Protective hinge in insulin opens to enable its receptor engagement.
Authors: Menting, J.G. / Yang, Y. / Chan, S.J. / Phillips, N.B. / Smith, B.J. / Whittaker, J. / Wickramasinghe, N.P. / Whittaker, L.J. / Pandyarajan, V. / Wan, Z.L. / Yadav, S.P. / Carroll, J.M. / ...Authors: Menting, J.G. / Yang, Y. / Chan, S.J. / Phillips, N.B. / Smith, B.J. / Whittaker, J. / Wickramasinghe, N.P. / Whittaker, L.J. / Pandyarajan, V. / Wan, Z.L. / Yadav, S.P. / Carroll, J.M. / Strokes, N. / Roberts, C.T. / Ismail-Beigi, F. / Milewski, W. / Steiner, D.F. / Chauhan, V.S. / Ward, C.W. / Weiss, M.A. / Lawrence, M.C.
History
DepositionJan 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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 / struct_asym / struct_conn / struct_ref_seq_dif / 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.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Insulin A chain
B: Insulin B chain
C: monoclonal antibody fab 83-7 fragment - heavy chain
D: monoclonal antibody fab 83-7 fragment - light chain
E: Insulin receptor domains L1-CR
F: Insulin receptor alpha-CT peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,68711
Polymers69,5426
Non-polymers2,1455
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.040, 169.040, 169.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23

-
Components

-
Protein/peptide , 2 types, 2 molecules AB

#1: Protein/peptide Insulin A chain / Insulin B chain / Insulin A chain


Mass: 2383.698 Da / Num. of mol.: 1 / Fragment: UNP residues 90-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P01308
#2: Protein/peptide Insulin B chain / Insulin B chain / Insulin A chain


Mass: 3433.953 Da / Num. of mol.: 1 / Fragment: UNP residues 25-54
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P01308

-
Insulin receptor ... , 2 types, 2 molecules EF

#5: Protein Insulin receptor domains L1-CR / IR / Insulin receptor subunit alpha / Insulin receptor subunit beta


Mass: 36231.762 Da / Num. of mol.: 1 / Fragment: L1-CR, UNP residues 28-377
Source method: isolated from a genetically manipulated source
Details: Lec 8 mutant CHO cell / Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Cell line (production host): Lec 8 mutant CHO cell / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06213
#6: Protein/peptide Insulin receptor alpha-CT peptide / IR / Insulin receptor subunit alpha / Insulin receptor subunit beta


Mass: 1922.143 Da / Num. of mol.: 1 / Fragment: alpha-CT peptide, UNP residues 731-746 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: P06213

-
Antibody , 2 types, 2 molecules CD

#3: Antibody monoclonal antibody fab 83-7 fragment - heavy chain


Mass: 12886.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Hybridoma cell / Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma cell / Production host: mus musculus (house mouse)
#4: Antibody monoclonal antibody fab 83-7 fragment - light chain


Mass: 12684.292 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Hybridoma cell / Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma cell / Production host: mus musculus (house mouse)

-
Sugars , 3 types, 5 molecules

#7: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-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
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/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
#8: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}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 / N-Acetylglucosamine


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 5.79 Å3/Da / Density % sol: 78.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.9-1.1M TRI-SODIUM CITRATE, 0.1M IMIDAZOLE-HCL, 0.02% SODIUM AZIDE, PH 8.0 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAustralian Synchrotron MX210.9537
SYNCHROTRONAustralian Synchrotron MX220.9537
SYNCHROTRONAustralian Synchrotron MX230.9537
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDDec 19, 2011
ADSC QUANTUM 315r2CCDApr 9, 2013
ADSC QUANTUM 315r3CCDApr 9, 2013
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DOUBLE CRYSTAL MONOCHROMATOR (SI111)SINGLE WAVELENGTHMx-ray1
2DOUBLE CRYSTAL MONOCHROMATOR (SI111)SINGLE WAVELENGTHMx-ray1
3DOUBLE CRYSTAL MONOCHROMATOR (SI111)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. all: 20608 / Num. obs: 20361 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -4 / Redundancy: 38.7 % / Biso Wilson estimate: 191.63 Å2 / Rmerge(I) obs: 0.214 / Net I/σ(I): 12.1
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 32.6 % / Rmerge(I) obs: 14.8 / Mean I/σ(I) obs: 0.17 / Num. unique all: 1609 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3W11
Resolution: 3.5→19.78 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.9193 / SU R Cruickshank DPI: 3.609 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2837 942 4.93 %RANDOM
Rwork0.2644 ---
all0.2654 20361 --
obs0.2654 19092 93.29 %-
Displacement parametersBiso mean: 238.45 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 1.177 Å
Refinement stepCycle: LAST / Resolution: 3.5→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4552 0 141 0 4693
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014827HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.316569HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1673SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes112HARMONIC2
X-RAY DIFFRACTIONt_gen_planes686HARMONIC5
X-RAY DIFFRACTIONt_it4827HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.93
X-RAY DIFFRACTIONt_other_torsion19.37
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion648SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5381SEMIHARMONIC4
LS refinement shellResolution: 3.5→3.69 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.1982 74 4.47 %
Rwork0.1943 1582 -
all0.1945 1656 -
obs-1656 93.29 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.9766-3.05512.91975.4575-6.785200.0474-0.3136-0.18650.442-0.2309-0.6788-0.25950.1390.18350.121-0.6504-0.4630.07380.63030.234436.404-42.5076-22.2233
210.319-5.34917.17446.0466-9.92778.2498-0.11760.04620.1388-0.36150.0137-0.4772-0.95840.43430.1040.099-0.6571-0.2937-0.28160.67960.626434.6289-46.535-31.1212
314.31922.14792.63197.2815-1.310411.19020.9961.1775-3.05531.0147-0.1701-2.30582.50641.7509-0.82590.62810.6702-0.912-0.7249-0.4290.937424.8252-110.292-23.5995
43.3333-0.4713-1.13097.6001-3.35316.64660.5614-0.192-1.01530.6029-0.22760.10410.79180.4117-0.33370.541-0.1093-0.4058-0.648-0.26960.4919.9367-103.762-9.511
54.20472.24720.96454.79360.17752.8284-0.15580.78180.4233-0.351-0.10620.0606-0.19420.42460.262-0.2159-0.10620.0506-0.14370.3363-0.036820.6221-69.6671-28.7514
60.1250.5567.317111.326110.069410.14660.0344-0.22790.33220.41420.2138-0.39580.18740.0694-0.24820.2852-0.3589-0.1269-0.03390.61090.110631.0312-51.272-21.9
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|21 }A1 - 21
2X-RAY DIFFRACTION2{ B|7 - B|27 }B7 - 27
3X-RAY DIFFRACTION3{ C|1 - C|118 }C1 - 118
4X-RAY DIFFRACTION4{ D|1 - D|114 }D1 - 114
5X-RAY DIFFRACTION5{ E|5 - E|310 E|501 - E|511 }E5 - 310
6X-RAY DIFFRACTION5{ E|5 - E|310 E|501 - E|511 }E501 - 511
7X-RAY DIFFRACTION6{ F|705 - F|719 }F705 - 719

+
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