[English] 日本語
Yorodumi
- PDB-7kd6: Insulin Receptor L1-CR plus alphaCT fragment in co-complex with F... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kd6
TitleInsulin Receptor L1-CR plus alphaCT fragment in co-complex with Fv 83-7 and single-chain insulin SCI-b
Components
  • (Insulin receptor ...) x 2
  • Fv 83-7 Heavy chain
  • Fv 83-7 Light chain
  • Single-chain Insulin SCI-b
KeywordsSIGNALING PROTEIN / Insulin receptor Single-chain insulin Antibody Fv module Insulin micro-receptor
Function / homology
Function and homology information


regulation of female gonad development / positive regulation of meiotic cell cycle / insulin-like growth factor II binding / positive regulation of developmental growth / male sex determination / insulin receptor complex / insulin-like growth factor I binding / positive regulation of protein-containing complex disassembly / insulin receptor activity / exocrine pancreas development ...regulation of female gonad development / positive regulation of meiotic cell cycle / insulin-like growth factor II binding / positive regulation of developmental growth / male sex determination / insulin receptor complex / insulin-like growth factor I binding / positive regulation of protein-containing complex disassembly / insulin receptor activity / exocrine pancreas development / dendritic spine maintenance / cargo receptor activity / insulin binding / adrenal gland development / neuronal cell body membrane / PTB domain binding / Signaling by Insulin receptor / IRS activation / positive regulation of respiratory burst / amyloid-beta clearance / positive regulation of receptor internalization / regulation of embryonic development / insulin receptor substrate binding / protein kinase activator activity / epidermis development / positive regulation of glycogen biosynthetic process / Signal attenuation / heart morphogenesis / transport across blood-brain barrier / phosphatidylinositol 3-kinase binding / Insulin receptor recycling / insulin-like growth factor receptor binding / dendrite membrane / neuron projection maintenance / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / receptor-mediated endocytosis / positive regulation of glycolytic process / positive regulation of D-glucose import / learning / receptor protein-tyrosine kinase / caveola / cellular response to growth factor stimulus / receptor internalization / memory / male gonad development / cellular response to insulin stimulus / positive regulation of nitric oxide biosynthetic process / insulin receptor signaling pathway / late endosome / glucose homeostasis / amyloid-beta binding / protein autophosphorylation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein tyrosine kinase activity / lysosome / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / endosome membrane / positive regulation of MAPK cascade / positive regulation of cell migration / G protein-coupled receptor signaling pathway / protein domain specific binding / axon / external side of plasma membrane / positive regulation of cell population proliferation / regulation of DNA-templated transcription / symbiont entry into host cell / GTP binding / positive regulation of DNA-templated transcription / protein-containing complex binding / extracellular exosome / ATP binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
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. / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain ...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. / 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 / Fibronectin type III domain / Growth factor receptor cysteine-rich domain superfamily / : / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLawrence, M.C. / Menting, J.G.
Funding support Australia, United States, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1058233 Australia
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01 DK040949 United States
CitationJournal: Biophys.J. / Year: 2022
Title: Single-chain insulin analogs threaded by the insulin receptor alpha CT domain.
Authors: Smith, N.A. / Menting, J.G. / Weiss, M.A. / Lawrence, M.C. / Smith, B.J.
History
DepositionOct 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Single-chain Insulin SCI-b
C: Fv 83-7 Heavy chain
D: Fv 83-7 Light chain
E: Insulin receptor subunit alpha
F: Insulin receptor isoform A alphaCT peptide
H: Single-chain Insulin SCI-b
I: Fv 83-7 Heavy chain
J: Fv 83-7 Light chain
K: Insulin receptor subunit alpha
L: Insulin receptor isoform A alphaCT peptide
N: Single-chain Insulin SCI-b
O: Fv 83-7 Heavy chain
P: Fv 83-7 Light chain
Q: Insulin receptor subunit alpha
R: Insulin receptor isoform A alphaCT peptide
T: Single-chain Insulin SCI-b
U: Fv 83-7 Heavy chain
V: Fv 83-7 Light chain
W: Insulin receptor subunit alpha
X: Insulin receptor isoform A alphaCT peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,39045
Polymers286,77020
Non-polymers8,62025
Water2,972165
1
B: Single-chain Insulin SCI-b
C: Fv 83-7 Heavy chain
D: Fv 83-7 Light chain
E: Insulin receptor subunit alpha
F: Insulin receptor isoform A alphaCT peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,56212
Polymers71,6925
Non-polymers2,8707
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: Single-chain Insulin SCI-b
I: Fv 83-7 Heavy chain
J: Fv 83-7 Light chain
K: Insulin receptor subunit alpha
L: Insulin receptor isoform A alphaCT peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,60911
Polymers71,6925
Non-polymers1,9176
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
N: Single-chain Insulin SCI-b
O: Fv 83-7 Heavy chain
P: Fv 83-7 Light chain
Q: Insulin receptor subunit alpha
R: Insulin receptor isoform A alphaCT peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,60911
Polymers71,6925
Non-polymers1,9176
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
T: Single-chain Insulin SCI-b
U: Fv 83-7 Heavy chain
V: Fv 83-7 Light chain
W: Insulin receptor subunit alpha
X: Insulin receptor isoform A alphaCT peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,60911
Polymers71,6925
Non-polymers1,9176
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.670, 128.430, 148.790
Angle α, β, γ (deg.)90.000, 90.180, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules BHNT

#1: Protein
Single-chain Insulin SCI-b


Mass: 6515.308 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Single-chain insulin SCI-b / Source: (gene. exp.) Homo sapiens (human) / Production host: Komagataella pastoris (fungus)

-
Insulin receptor ... , 2 types, 8 molecules EKQWFLRX

#4: Protein
Insulin receptor subunit alpha / IR


Mass: 36231.762 Da / Num. of mol.: 4 / Mutation: Y171H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Plasmid: pEE14 / Cell line (production host): Lec 8 mutant / Organ (production host): Ovary / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P06213, receptor protein-tyrosine kinase
#5: Protein/peptide
Insulin receptor isoform A alphaCT peptide


Mass: 1922.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: receptor protein-tyrosine kinase

-
Antibody , 2 types, 8 molecules CIOUDJPV

#2: Antibody
Fv 83-7 Heavy chain


Mass: 13655.276 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Brevibacillus brevis (bacteria)
#3: Antibody
Fv 83-7 Light chain


Mass: 13367.913 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Brevibacillus brevis (bacteria)

-
Sugars , 4 types, 20 molecules

#6: 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.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#7: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#8: 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.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#11: 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.: 10 / Source method: obtained synthetically / 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 , 3 types, 170 molecules

#9: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.45 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16% PEG 3350, 0.2 M sodium thiocyanate (NaSCN), 0.02% sodium azide (NaN3)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→45.67 Å / Num. obs: 112001 / % possible obs: 88.2 % / Redundancy: 3.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.216 / Net I/av σ(I): 6.1 / Net I/σ(I): 6.1
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 3.32 / Num. unique obs: 11764 / CC1/2: 0.168

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OGA

4oga


Resolution: 2.6→45.65 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.365 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.341 / SU Rfree Blow DPI: 0.231 / SU Rfree Cruickshank DPI: 0.239
RfactorNum. reflection% reflectionSelection details
Rfree0.221 5626 5.08 %RANDOM
Rwork0.189 ---
obs0.191 110844 98.2 %-
Displacement parametersBiso max: 210.94 Å2 / Biso mean: 87.37 Å2 / Biso min: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.4735 Å20 Å21.5052 Å2
2---17.8071 Å20 Å2
3---16.3336 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: final / Resolution: 2.6→45.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18341 0 561 165 19067
Biso mean--119.48 50.06 -
Num. residues----2324
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6731SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3224HARMONIC5
X-RAY DIFFRACTIONt_it19441HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2593SEMIHARMONIC5
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_contact20835SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d19441HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg26446HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion3.37
X-RAY DIFFRACTIONt_other_torsion19.04
LS refinement shellResolution: 2.6→2.62 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3187 112 5.05 %
Rwork0.253 2105 -
all0.2564 2217 -
obs--75.66 %
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)
14.40370.82090.07980.9635-2.00146.3733-0.0341-0.5144-0.17880.43260.0167-0.17260.1294-0.04270.0174-0.02830.09130.04420.3062-0.1406-0.3069110.914410.491648.4304
22.622-0.2048-1.06680.85510.28323.46690.03720.320.14750.147-0.084-0.0444-0.10340.21770.0468-0.22460.00930.05110.2757-0.0194-0.0919137.6726-1.7476-13.3335
34.49921.35081.25032.30511.26174.46460.09680.3691-0.34180.0985-0.09480.39980.5378-0.5504-0.002-0.2791-0.05240.09440.2035-0.0575-0.0886118.3892-12.069-14.8227
41.4672-0.8866-0.80041.35510.90662.4153-0.03350.08310.19190.0756-0.10730.0525-0.02140.0160.1408-0.198-0.0290.09060.1217-0.056-0.1633113.156810.872918.7054
5-0.0007-3.74970.10640-0.59465.9553-0.005-0.0571-0.0949-0.12520.1145-0.20160.1535-0.0115-0.10950.1625-0.00760.09760.1251-0.0119-0.2251110.43016.977639.3007
65.19510.41230.58313.1454-1.65568.3164-0.01780.3133-0.4538-0.22690.17730.1152-0.1239-0.2584-0.1595-0.0192-0.14190.14920.27460.0918-0.307386.99397.2665-99.0027
72.97540.3589-0.31871.29530.73173.87320.01780.1328-0.0158-0.2129-0.23330.0564-0.086-0.47040.2155-0.18620.00520.02520.1665-0.002-0.081368.0702-11.0675-35.6082
84.3183-1.39650.45362.3195-1.41114.12350.136-0.0882-0.1435-0.2658-0.17-0.77090.21140.59130.0341-0.27990.01070.11870.08580.04480.024688.5291-18.176-36.1181
91.13971.5376-1.91362.9964-2.28084.7720.02340.02280.1268-0.2748-0.0353-0.0282-0.2106-0.21660.0119-0.09040.12620.1632-0.03670.0871-0.323586.25396.4193-68.8658
100.11160.0026-3.45930.9396-0.57574.6373-0.00770.036-0.178-0.03640.08580.1270.102-0.0124-0.07810.2464-0.14260.28640.0296-0.0091-0.232689.29913.2639-90.8301
113.1336-1.9414-1.82630.0744-0.51259.27090.0683-0.3850.14540.17070.13010.21640.09290.0849-0.19840.30560.0108-0.28180.25030.0678-0.34394.9352-16.507548.7803
123.43860.16421.64670.55650.34154.1074-0.1202-0.24010.37840.1333-0.06750.0449-0.1665-0.35570.1877-0.2437-0.0105-0.00890.2614-0.0505-0.099668.7741-2.5897-13.1927
134.73931.4361.47382.9677-1.42597.4511-0.24170.48480.42210.1359-0.0676-0.5595-0.78760.8490.3093-0.3406-0.2035-0.09450.35910.0123-0.040788.257.2549-14.4553
142.0615-0.35471.61931.82560.154.34570.3074-0.1622-0.23470.6158-0.1771-0.35250.9888-0.4108-0.1303-0.0118-0.1074-0.2774-0.09360.0123-0.314892.8428-16.821918.4077
15-0.0199-2.29383.15080.4583-0.00995.3787-0.0054-0.0610.14590.04440.05150.1914-0.0718-0.0311-0.04610.3679-0.0248-0.30180.0868-0.004-0.318495.937-12.881439.5389
161.18280.0837-2.10592.0911.09296.4446-0.01980.11360.3051-0.4209-0.0540.12890.18090.26360.07380.20650.0915-0.2010.3715-0.0688-0.3955119.2989-14.7131-99.0958
173.49471.16241.91152.60640.62174.4479-0.32130.53590.3855-0.49130.03950.0507-0.31870.72450.2818-0.2775-0.1139-0.02920.40120.1007-0.282138.47836.6578-36.1811
183.9621-0.9693-0.17623.81312.55544.7852-0.15250.19420.509-0.8227-0.24811.0859-0.6863-0.03230.4006-0.33610.0046-0.30570.06790.09270.1969118.368414.2668-36.8717
191.84371.23022.98082.14342.29318.519-0.14940.2985-0.0034-0.1561-0.27560.27170.28750.8820.425-0.08740.0993-0.1360.08380.0009-0.3843119.0959-12.3593-67.8869
200.3871-0.37833.77920.306-2.08255.0154-0.00570.08010.1318-0.0239-0.003-0.0362-0.03850.08020.00870.3482-0.1445-0.30180.1576-0.006-0.3444116.7985-9.9681-90.0496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|1 - B|57 }B1 - 57
2X-RAY DIFFRACTION2{ C|0 - C|123 }C0 - 123
3X-RAY DIFFRACTION3{ D|-2 - D|113 }D-2 - 113
4X-RAY DIFFRACTION4{ E|6 - E|310 }E6 - 310
5X-RAY DIFFRACTION5{ F|704 - F|718 }F704 - 718
6X-RAY DIFFRACTION6{ H|1 - H|57 }H1 - 57
7X-RAY DIFFRACTION7{ I|0 - I|122 }I0 - 122
8X-RAY DIFFRACTION8{ J|-1 - J|113 }J-1 - 113
9X-RAY DIFFRACTION9{ K|5 - K|303 }K5 - 303
10X-RAY DIFFRACTION10{ L|704 - L|718 }L704 - 718
11X-RAY DIFFRACTION11{ N|1 - N|57 }N1 - 57
12X-RAY DIFFRACTION12{ O|0 - O|123 }O0 - 123
13X-RAY DIFFRACTION13{ P|-2 - P|112 }P-2 - 112
14X-RAY DIFFRACTION14{ Q|5 - Q|310 }Q5 - 310
15X-RAY DIFFRACTION15{ R|704 - R|718 }R704 - 718
16X-RAY DIFFRACTION16{ T|1 - T|57 }T1 - 57
17X-RAY DIFFRACTION17{ U|0 - U|119 }U0 - 119
18X-RAY DIFFRACTION18{ V|-1 - V|112 }V-1 - 112
19X-RAY DIFFRACTION19{ W|3 - W|303 }W3 - 303
20X-RAY DIFFRACTION20{ X|704 - X|717 }X704 - 717

+
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