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- PDB-5kqv: Insulin receptor ectodomain construct comprising domains L1,CR,L2... -

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Basic information

Entry
Database: PDB / ID: 5kqv
TitleInsulin receptor ectodomain construct comprising domains L1,CR,L2, FnIII-1 and alphaCT peptide in complex with bovine insulin and FAB 83-14 (REVISED STRUCTURE)
Components
  • (Insulin) x 2
  • (MONOCLONAL ANTIBODY FAB 83-14 - ...) x 2
  • Insulin receptor,Insulin receptor
KeywordsHormone/Hormone Receptor/Immune System / Cell surface receptor/immune system / insulin receptor / IR ectodomain / CT peptide / HORMONE-HORMONE RECEPTOR-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


estradiol secretion / negative regulation of lactation / positive regulation of blood circulation / glucose import in response to insulin stimulus / positive regulation of cell maturation / positive regulation of lactation / response to L-arginine / positive regulation of mammary gland epithelial cell proliferation / regulation of female gonad development / positive regulation of meiotic cell cycle ...estradiol secretion / negative regulation of lactation / positive regulation of blood circulation / glucose import in response to insulin stimulus / positive regulation of cell maturation / positive regulation of lactation / response to L-arginine / positive regulation of mammary gland epithelial cell proliferation / regulation of female gonad development / positive regulation of meiotic cell cycle / negative regulation of appetite / response to butyrate / 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 / feeding behavior / positive regulation of protein-containing complex disassembly / response to growth hormone / cargo receptor activity / response to food / dendritic spine maintenance / insulin binding / PTB domain binding / positive regulation of Rho protein signal transduction / neuronal cell body membrane / adrenal gland development / Signaling by Insulin receptor / IRS activation / amyloid-beta clearance / positive regulation of peptide hormone secretion / activation of protein kinase activity / positive regulation of respiratory burst / regulation of embryonic development / positive regulation of receptor internalization / transport across blood-brain barrier / protein secretion / insulin receptor substrate binding / epidermis development / positive regulation of glycogen biosynthetic process / Signal attenuation / response to glucose / phosphatidylinositol 3-kinase binding / negative regulation of lipid catabolic process / heart morphogenesis / dendrite membrane / Insulin receptor recycling / insulin-like growth factor receptor binding / receptor-mediated endocytosis / neuron projection maintenance / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / response to nutrient levels / positive regulation of mitotic nuclear division / learning / caveola / positive regulation of protein secretion / positive regulation of glucose import / positive regulation of MAP kinase activity / insulin receptor binding / hormone activity / receptor internalization / positive regulation of insulin secretion / receptor protein-tyrosine kinase / memory / cellular response to growth factor stimulus / peptidyl-tyrosine phosphorylation / cellular response to insulin stimulus / male gonad development / cell surface receptor protein tyrosine kinase signaling pathway / glucose metabolic process / positive regulation of nitric oxide biosynthetic process / late endosome / glucose homeostasis / insulin receptor signaling pathway / amyloid-beta binding / response to heat / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein tyrosine kinase activity / positive regulation of MAPK cascade / protein autophosphorylation / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / endosome membrane / carbohydrate metabolic process / positive regulation of cell migration / positive regulation of protein phosphorylation / symbiont entry into host cell / G protein-coupled receptor signaling pathway / axon / protein domain specific binding / external side of plasma membrane / protein phosphorylation / positive regulation of cell population proliferation / protein-containing complex binding
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. / Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. ...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. / 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 / 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 / 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
Similarity search - Domain/homology
Insulin / Insulin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.4 Å
AuthorsLawrence, M.C. / Smith, B.J. / Croll, T.I.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1005896 Australia
Citation
Journal: Nature / Year: 2013
Title: How insulin engages its primary binding site on the insulin receptor.
Authors: Menting, J.G. / Whittaker, J. / Margetts, M.B. / Whittaker, L.J. / Kong, G.K. / Smith, B.J. / Watson, C.J. / Zakova, L. / Kletvikova, E. / Jiracek, J. / Chan, S.J. / Steiner, D.F. / Dodson, ...Authors: Menting, J.G. / Whittaker, J. / Margetts, M.B. / Whittaker, L.J. / Kong, G.K. / Smith, B.J. / Watson, C.J. / Zakova, L. / Kletvikova, E. / Jiracek, J. / Chan, S.J. / Steiner, D.F. / Dodson, G.G. / Brzozowski, A.M. / Weiss, M.A. / Ward, C.W. / Lawrence, M.C.
#1: Journal: Structure / Year: 2016
Title: Higher-Resolution Structure of the Human Insulin Receptor Ectodomain: Multi-Modal Inclusion of the Insert Domain.
Authors: Croll, T.I. / Smith, B.J. / Margetts, M.B. / Whittaker, J. / Weiss, M.A. / Ward, C.W. / Lawrence, M.C.
History
DepositionJul 6, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionJul 19, 2017ID: 3W14
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin
B: Insulin
C: MONOCLONAL ANTIBODY FAB 83-14 - HEAVY CHAIN
D: MONOCLONAL ANTIBODY FAB 83-14 - LIGHT CHAIN
E: Insulin receptor,Insulin receptor
F: Insulin receptor,Insulin receptor
I: Insulin
J: Insulin
P: MONOCLONAL ANTIBODY FAB 83-14 - HEAVY CHAIN
Q: MONOCLONAL ANTIBODY FAB 83-14 - LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,02713
Polymers245,72210
Non-polymers1,3053
Water0
1
A: Insulin
B: Insulin
C: MONOCLONAL ANTIBODY FAB 83-14 - HEAVY CHAIN
D: MONOCLONAL ANTIBODY FAB 83-14 - LIGHT CHAIN
E: Insulin receptor,Insulin receptor
F: Insulin receptor,Insulin receptor
I: Insulin
J: Insulin
P: MONOCLONAL ANTIBODY FAB 83-14 - HEAVY CHAIN
Q: MONOCLONAL ANTIBODY FAB 83-14 - LIGHT CHAIN
hetero molecules

A: Insulin
B: Insulin
C: MONOCLONAL ANTIBODY FAB 83-14 - HEAVY CHAIN
D: MONOCLONAL ANTIBODY FAB 83-14 - LIGHT CHAIN
E: Insulin receptor,Insulin receptor
F: Insulin receptor,Insulin receptor
I: Insulin
J: Insulin
P: MONOCLONAL ANTIBODY FAB 83-14 - HEAVY CHAIN
Q: MONOCLONAL ANTIBODY FAB 83-14 - LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)494,05426
Polymers491,44420
Non-polymers2,6106
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)118.150, 140.100, 190.022
Angle α, β, γ (deg.)90.00, 95.04, 90.00
Int Tables number5
Space group name H-MI121

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Components

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Protein/peptide , 2 types, 4 molecules AIBJ

#1: Protein/peptide Insulin /


Mass: 2339.645 Da / Num. of mol.: 2 / Fragment: UNP Residues 85-105 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P01317
#2: Protein/peptide Insulin /


Mass: 3403.927 Da / Num. of mol.: 2 / Fragment: UNP Residues 25-54 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P01317

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Protein , 1 types, 2 molecules EF

#5: Protein Insulin receptor,Insulin receptor / IR / IR


Mass: 69979.859 Da / Num. of mol.: 2 / Mutation: Y144H,Y144H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Plasmid: PEE14 / Cell line (production host): Lec8 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P06213, receptor protein-tyrosine kinase

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Antibody , 2 types, 4 molecules CPDQ

#3: Antibody MONOCLONAL ANTIBODY FAB 83-14 - HEAVY CHAIN


Mass: 23622.672 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Plasmid details: hybridoma
#4: Antibody MONOCLONAL ANTIBODY FAB 83-14 - LIGHT CHAIN


Mass: 23514.807 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Plasmid details: hybridoma

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Sugars , 2 types, 3 molecules

#6: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 9% POLYETHYLENE GLYCOL 3350, 200MM PROLINE, 100MM HEPES/NAOH, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953691 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953691 Å / Relative weight: 1
ReflectionResolution: 4.4→50 Å / Num. obs: 17344 / % possible obs: 87.7 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 182.16 Å2 / Rmerge(I) obs: 0.206 / Net I/σ(I): 2.77
Reflection shellResolution: 4.4→4.5 Å / Redundancy: 2.8 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 0.78 / Num. unique obs: 1064 / % possible all: 84.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZXB

4zxb


Resolution: 4.4→42.49 Å / Cor.coef. Fo:Fc: 0.9144 / Cor.coef. Fo:Fc free: 0.8767 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 1.152
Details: The apparent discrepancy in calculated Rwork/Rfree from reported by depositor is use of expectation values in calculation by BUSTER
RfactorNum. reflection% reflectionSelection details
Rfree0.2663 886 5.11 %RANDOM
Rwork0.2287 ---
obs0.2307 17331 88.06 %-
Displacement parametersBiso mean: 247.62 Å2
Baniso -1Baniso -2Baniso -3
1-9.8121 Å20 Å27.2191 Å2
2--17.2601 Å20 Å2
3----27.0722 Å2
Refine analyzeLuzzati coordinate error obs: 1.5 Å
Refinement stepCycle: 1 / Resolution: 4.4→42.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16649 0 86 0 16735
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0117188HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3723376HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5848SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes402HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2470HARMONIC5
X-RAY DIFFRACTIONt_it17188HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.32
X-RAY DIFFRACTIONt_other_torsion19.42
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2264SEMIHARMONIC5
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_contact18482SEMIHARMONIC4
LS refinement shellResolution: 4.4→4.67 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2611 141 5.1 %
Rwork0.2271 2626 -
all0.2289 2767 -
obs--88.06 %
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)
14.2687-1.26323.01890.2629-4.266610.298-0.10970.37060.70331.4651-1.0117-0.2025-2.40363.09431.12140.6861-0.9426-0.46250.53020.1724-0.366895.2548-34.706618.7176
27.0828-1.5947-4.015211.6285-3.922912.48770.5267-0.2801-0.4684-0.7409-0.55030.0056-0.88450.06670.02360.1926-0.1909-0.3625-0.41650.31720.286156.4632-68.881632.1093
314.52070.6736-0.81576.6061-1.80724.29390.2148-0.35820.86890.1711-0.34850.758-0.6798-0.27160.13370.5886-0.09170.0468-0.59190.271-0.103548.1804-98.947928.2918
44.64310.3491-3.399711.8351-6.225221.956-0.179-0.1739-0.14231.7422-0.2387-0.6115-0.8971-0.06130.41770.5867-0.1219-0.2423-0.6395-0.2473-0.542250.7754-116.90546.5977
53.16651.456-0.741322.7756-9.57420.1420.3539-0.0353-0.63650.3953-0.4737-0.91891.21851.21080.11980.34280.1444-0.30780.05730.34910.201354.969-152.49955.6975
64.46696.8921.561820.10250.742211.37670.30790.5209-0.3118-1.1462-0.17411.50490.53030.1037-0.1338-0.068-0.2237-0.0976-0.40170.0087-0.352646.9137-127.75126.44
74.65637.08441.418120.5945-3.71457.6052-0.246-0.36040.17950.1898-0.0819-0.15151.8248-0.00270.32790.69470.0472-0.4256-0.3373-0.01590.081141.1994-153.28549.3841
83.9657-5.3439-3.000919.16397.149616.5421.59781.6692-1.652-3.7328-3.22694.2984-2.6146-3.62011.6291-0.08430.7157-1.31960.4033-1.13490.580129.0305-120-27.1945
914.6275-3.6928-8.51539.3791-3.9417.2306-0.00790.7531-0.5214-0.5647-0.16790.54121.5611-0.55360.17580.62760.109-0.4632-0.729-0.330.164929.8674-85.093312.0628
106.13530.48274.04216.8315-5.41767.01030.361-0.6863-1.31660.47350.00840.12340.78890.1418-0.36940.21390.33170.0995-0.47460.06950.106535.6069-56.136421.6442
1115.6721-3.6692-2.748716.98334.325710.35320.07870.1692-0.0115-0.17420.12741.8271-0.8145-0.2648-0.2062-0.2829-0.2455-0.1367-0.64110.2244-0.1918.0952-36.101423.4775
1212.5385-1.0989-2.965511.5958-0.20526.8940.4921.74742.3685-1.08450.2266-0.7367-1.0297-0.9823-0.71860.01960.35880.0692-0.25370.17610.28287.7034-0.498222.6933
1312.95721.88060.21937.65644.55825.20890.10010.33710.244-0.2025-0.2776-1.1289-0.32560.61390.1775-0.0287-0.00410.0134-0.3829-0.136-0.626738.409-25.477120.4355
147.5206-10.0498-2.62214.42133.02616.4501-0.0466-0.72371.10330.10480.5331-0.4155-1.32681.0587-0.4866-0.0469-0.1925-0.2478-0.1355-0.610.89517.9510.431334.0931
1510.73915.067814.12130-4.85115.33280.28910.3921-0.26790.5547-0.8167-0.375-1.599-0.71630.52751.34850.0663-0.4376-0.5273-0.4308-0.075259.8804-29.9243.5802
1614.12624.65188.213606.24331.33890.2336-0.2501-0.4124-0.2738-0.38290.05670.00890.52050.1493-0.20750.0899-0.4211-0.33470.06010.872555.5977-123.8440.784
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ E|4 - E|310 }
2X-RAY DIFFRACTION2{ E|311 - E|469 }
3X-RAY DIFFRACTION3{ E|470 - E|593 }
4X-RAY DIFFRACTION4{ D|1 - D|107 }
5X-RAY DIFFRACTION5{ D|108 - D|214 }
6X-RAY DIFFRACTION6{ C|1 - C|117 }
7X-RAY DIFFRACTION7{ C|118 - C|207 }
8X-RAY DIFFRACTION8{ F|4 - F|310 }
9X-RAY DIFFRACTION9{ F|311 - F|469 }
10X-RAY DIFFRACTION10{ F|470 - F|593 }
11X-RAY DIFFRACTION11{ Q|1 - Q|107 }
12X-RAY DIFFRACTION12{ Q|108 - Q|214 }
13X-RAY DIFFRACTION13{ P|1 - P|117 }
14X-RAY DIFFRACTION14{ P|118 - P|207 }
15X-RAY DIFFRACTION15{ A|* B|* F|594 - F|605 }
16X-RAY DIFFRACTION16{ I|* J|* E|594 - E|605 }

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Yorodumi

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  • 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

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