[English] 日本語
Yorodumi
- PDB-3u7u: Crystal structure of extracellular region of human epidermal grow... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3u7u
TitleCrystal structure of extracellular region of human epidermal growth factor receptor 4 in complex with neuregulin-1 beta
Components
  • Neuregulin 1
  • Receptor tyrosine-protein kinase erbB-4
KeywordsTRANSFERASE/TRANSFERASE REGULATOR / signaling protein / TRANSFERASE-TRANSFERASE REGULATOR COMPLEX / Glycosylation
Function / homology
Function and homology information


ERBB3 signaling pathway / positive regulation of peptidyl-tyrosine autophosphorylation / sequestering of metal ion / establishment of planar polarity involved in nephron morphogenesis / ERBB4 signaling pathway / ERBB4-ERBB4 signaling pathway / olfactory bulb interneuron differentiation / central nervous system morphogenesis / ventricular cardiac muscle cell differentiation / positive regulation of striated muscle cell differentiation ...ERBB3 signaling pathway / positive regulation of peptidyl-tyrosine autophosphorylation / sequestering of metal ion / establishment of planar polarity involved in nephron morphogenesis / ERBB4 signaling pathway / ERBB4-ERBB4 signaling pathway / olfactory bulb interneuron differentiation / central nervous system morphogenesis / ventricular cardiac muscle cell differentiation / positive regulation of striated muscle cell differentiation / neuregulin receptor activity / negative regulation of secretion / cardiac muscle tissue regeneration / animal organ development / endocardial cell differentiation / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / mitochondrial fragmentation involved in apoptotic process / neural crest cell development / cardiac muscle cell myoblast differentiation / cell communication / GABA receptor binding / PI3K events in ERBB4 signaling / cardiac muscle cell differentiation / mammary gland epithelial cell differentiation / embryonic pattern specification / mammary gland development / chemorepellent activity / ventricular trabecula myocardium morphogenesis / positive regulation of protein localization to cell surface / ErbB-3 class receptor binding / regulation of postsynaptic neurotransmitter receptor internalization / neurotransmitter receptor localization to postsynaptic specialization membrane / ERBB signaling pathway / activation of transmembrane receptor protein tyrosine kinase activity / neural crest cell migration / epidermal growth factor receptor activity / negative regulation of cardiac muscle cell apoptotic process / epidermal growth factor receptor binding / ERBB2 Activates PTK6 Signaling / ERBB2-ERBB3 signaling pathway / transmembrane receptor protein tyrosine kinase activator activity / protein tyrosine kinase activator activity / Signaling by ERBB4 / ERBB2 Regulates Cell Motility / cell surface receptor signaling pathway via JAK-STAT / Long-term potentiation / PI3K events in ERBB2 signaling / positive regulation of cell adhesion / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / SHC1 events in ERBB4 signaling / GABA-ergic synapse / mammary gland alveolus development / cell fate commitment / Nuclear signaling by ERBB4 / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of cardiac muscle cell proliferation / Signaling by ERBB2 / regulation of cell migration / cellular response to epidermal growth factor stimulus / cell surface receptor protein tyrosine kinase signaling pathway / synapse assembly / Downregulation of ERBB4 signaling / lactation / GRB2 events in ERBB2 signaling / Downregulation of ERBB2:ERBB3 signaling / activation of protein kinase B activity / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / neurogenesis / basal plasma membrane / cytokine activity / transcription coregulator activity / postsynaptic density membrane / Signaling by ERBB2 TMD/JMD mutants / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / wound healing / positive regulation of protein-containing complex assembly / neuromuscular junction / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / Downregulation of ERBB2 signaling / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / integrin binding / PIP3 activates AKT signaling / presynaptic membrane / nervous system development / heart development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of cell growth / basolateral plasma membrane / postsynaptic membrane / protein tyrosine kinase activity / Estrogen-dependent gene expression / cell population proliferation
Similarity search - Function
Neuregulin, C-terminal / Neuregulin-1 / Neuregulin / Neuregulin intracellular region / 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 / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment ...Neuregulin, C-terminal / Neuregulin-1 / Neuregulin / Neuregulin intracellular region / 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 / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Alpha-Beta Horseshoe / Laminin / Laminin / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / EGF-like domain / Furin-like repeat / Furin-like repeats / Immunoglobulin I-set / Immunoglobulin I-set domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Ribbon / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / 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 / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Pro-neuregulin-1, membrane-bound isoform / Receptor tyrosine-protein kinase erbB-4 / Neuregulin 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.03 Å
AuthorsLiu, P. / Cleveland IV, T.E. / Bouyain, S. / Longo, P.A. / Leahy, D.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: A single ligand is sufficient to activate EGFR dimers.
Authors: Liu, P. / Cleveland, T.E. / Bouyain, S. / Byrne, P.O. / Longo, P.A. / Leahy, D.J.
History
DepositionOct 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 13, 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: Receptor tyrosine-protein kinase erbB-4
B: Receptor tyrosine-protein kinase erbB-4
C: Receptor tyrosine-protein kinase erbB-4
D: Receptor tyrosine-protein kinase erbB-4
E: Receptor tyrosine-protein kinase erbB-4
F: Receptor tyrosine-protein kinase erbB-4
G: Neuregulin 1
H: Neuregulin 1
I: Neuregulin 1
J: Neuregulin 1
K: Neuregulin 1
L: Neuregulin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)455,34138
Polymers449,59012
Non-polymers5,75126
Water5,242291
1
A: Receptor tyrosine-protein kinase erbB-4
G: Neuregulin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8166
Polymers74,9322
Non-polymers8854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint4 kcal/mol
Surface area29690 Å2
MethodPISA
2
B: Receptor tyrosine-protein kinase erbB-4
H: Neuregulin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2598
Polymers74,9322
Non-polymers1,3276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint12 kcal/mol
Surface area33360 Å2
MethodPISA
3
C: Receptor tyrosine-protein kinase erbB-4
I: Neuregulin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3744
Polymers74,9322
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint1 kcal/mol
Surface area32450 Å2
MethodPISA
4
D: Receptor tyrosine-protein kinase erbB-4
J: Neuregulin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0387
Polymers74,9322
Non-polymers1,1065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint9 kcal/mol
Surface area32910 Å2
MethodPISA
5
E: Receptor tyrosine-protein kinase erbB-4
K: Neuregulin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5955
Polymers74,9322
Non-polymers6643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint5 kcal/mol
Surface area32200 Å2
MethodPISA
6
F: Receptor tyrosine-protein kinase erbB-4
L: Neuregulin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2598
Polymers74,9322
Non-polymers1,3276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint13 kcal/mol
Surface area32890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.730, 223.510, 146.920
Angle α, β, γ (deg.)90.00, 99.72, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Receptor tyrosine-protein kinase erbB-4 / Proto-oncogene-like protein c-ErbB-4 / Tyrosine kinase-type cell surface receptor HER4 / p180erbB4 ...Proto-oncogene-like protein c-ErbB-4 / Tyrosine kinase-type cell surface receptor HER4 / p180erbB4 / ERBB4 intracellular domain / 4ICD / E4ICD / s80HER4


Mass: 68735.508 Da / Num. of mol.: 6 / Fragment: Extracellular region (UNP Residues 26-640)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB4, HER4 / Plasmid: pSGHV0 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Lec 3.2.8.1
References: UniProt: Q15303, receptor protein-tyrosine kinase
#2: Protein
Neuregulin 1


Mass: 6196.122 Da / Num. of mol.: 6 / Fragment: EGF-like domain (UNP Residues 230-284)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRG1 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96IB3, UniProt: Q02297*PLUS
#3: 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.: 26
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG6000, Mg(OAc)2, MES pH6.0, Hampton Silver Bullet, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.98011 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2010
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 3.03→50 Å / Num. all: 104051 / Num. obs: 104051 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 93.35 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.03-3.082.70.685187
3.08-3.1430.634194.4
3.14-3.23.40.554198
3.2-3.263.60.51199.5
3.26-3.333.80.441199.9
3.33-3.413.80.365199.8
3.41-3.53.80.326199.8
3.5-3.593.90.236199.9
3.59-3.73.80.216199.9
3.7-3.823.90.167199.9
3.82-3.953.80.155199.9
3.95-4.113.90.119199.9
4.11-4.33.90.1031100
4.3-4.533.90.0871100
4.53-4.813.90.0761100
4.81-5.183.90.0731100
5.18-5.73.90.078199.9
5.7-6.523.90.081100
6.52-8.213.90.0661100
8.21-503.80.069199.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
JBluIce-EPICSdata collection
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTREIS 1MOX AND 2AHX
Resolution: 3.03→49.63 Å / Cor.coef. Fo:Fc: 0.9316 / Cor.coef. Fo:Fc free: 0.9044 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 5198 5 %RANDOM
Rwork0.1895 ---
obs0.1914 103996 --
all-103996 --
Displacement parametersBiso mean: 91 Å2
Baniso -1Baniso -2Baniso -3
1-4.2937 Å20 Å2-3.5897 Å2
2--7.8176 Å20 Å2
3----12.1114 Å2
Refine analyzeLuzzati coordinate error obs: 0.544 Å
Refinement stepCycle: LAST / Resolution: 3.03→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29872 0 364 291 30527
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0131022HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2642091HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d10587SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes872HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4525HARMONIC5
X-RAY DIFFRACTIONt_it31022HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion19.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4174SEMIHARMONIC5
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_contact33541SEMIHARMONIC4
LS refinement shellResolution: 3.03→3.11 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 307 4.64 %
Rwork0.2609 6316 -
all0.2629 6623 -
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)
11.36610.9214-0.06061.65080.13051.48490.03880.3127-0.26650.11020.1651-0.19550.44110.0851-0.2039-0.30710.176-0.0966-0.1614-0.1104-0.0688-3.0173-44.03923.261
20.7736-0.24270.31671.0834-0.35870.8593-0.0208-0.01840.07570.1891-0.12220.02-0.0319-0.15950.143-0.211-0.02640.099-0.12330.0095-0.077517.8972-12.974357.6662
30.7610.25830.36531.02840.37331.8413-0.15710.2290.2461-0.2789-0.0650.0704-0.4273-0.22310.2221-0.29430.0395-0.0172-0.06420.1248-0.0512-60.39043.3158-6.4105
40.7128-0.311-0.25770.89620.10451.8764-0.03640.0219-0.1145-0.02480.02530.20880.3670.21060.0111-0.28290.001-0.043-0.19150.0074-0.0411-39.7135-39.85137.4642
50.83821.00330.22831.69480.63651.1464-0.26390.440.2045-0.4110.37720.3125-0.31450.329-0.1133-0.349-0.1033-0.02720.10250.2608-0.0847-12.604517.23388.0565
60.943-0.5392-0.30691.48860.11490.95240.016-0.10140.11950.1867-0.00140.0256-0.17330.2473-0.0147-0.2356-0.0836-0.0118-0.14850.0039-0.0486-32.55097.255652.316
70.20310.97431.75371.99940.90631.6642-0.01080.2832-0.2119-0.17140.1563-0.25650.15020.2899-0.1455-0.1720.18290.0406-0.0788-0.28870.23458.0127-56.06144.4922
80.4362-1.37120.73943.3848-1.21253.33180.0238-0.230.11140.3095-0.05380.2212-0.1843-0.37950.03-0.05980.25430.1203-0.0197-0.16140.02375.221612.279767.188
90.35041.39170.01382.77870.58622.25020.0570.13710.1164-0.1399-0.0489-0.0937-0.46270.1235-0.00810.1922-0.1334-0.1495-0.29730.29050.0467-49.587828.5483-2.6764
101.27120.416-2.04541.1197-2.04642.7880.00410.0078-0.19180.2196-0.09410.2570.4019-0.02910.090.1925-0.10070.2802-0.4444-0.00830.3271-51.3478-60.774224.7167
11-0.6371-0.07431.53194.143-0.41023.825-0.00210.09850.0969-0.2607-0.01610.1156-0.1334-0.00830.0181-0.1007-0.3138-0.30790.24960.2662-0.171-23.296612.4273-17.6639
12-0.139-1.22830.19373.20530.0812.6502-0.0576-0.2790.0770.25950.0021-0.08510.11830.49960.0555-0.09540.0946-0.15890.2506-0.0142-0.2233-20.7346-7.469773.5791
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|145 A|148 - A|154 A|159 - A|556 A|1001 - A|1004 }A1 - 145
2X-RAY DIFFRACTION1{ A|1 - A|145 A|148 - A|154 A|159 - A|556 A|1001 - A|1004 }A148 - 154
3X-RAY DIFFRACTION1{ A|1 - A|145 A|148 - A|154 A|159 - A|556 A|1001 - A|1004 }A159 - 556
4X-RAY DIFFRACTION1{ A|1 - A|145 A|148 - A|154 A|159 - A|556 A|1001 - A|1004 }A1001 - 1004
5X-RAY DIFFRACTION2{ B|1 - B|145 B|148 - B|154 B|159 - B|572 B|578 - B|612 B|1001 - B|1006 }B1 - 145
6X-RAY DIFFRACTION2{ B|1 - B|145 B|148 - B|154 B|159 - B|572 B|578 - B|612 B|1001 - B|1006 }B148 - 154
7X-RAY DIFFRACTION2{ B|1 - B|145 B|148 - B|154 B|159 - B|572 B|578 - B|612 B|1001 - B|1006 }B159 - 572
8X-RAY DIFFRACTION2{ B|1 - B|145 B|148 - B|154 B|159 - B|572 B|578 - B|612 B|1001 - B|1006 }B578 - 612
9X-RAY DIFFRACTION2{ B|1 - B|145 B|148 - B|154 B|159 - B|572 B|578 - B|612 B|1001 - B|1006 }B1001 - 1006
10X-RAY DIFFRACTION3{ C|1 - C|145 C|148 - C|154 C|158 - C|572 C|579 - C|609 C|1001 - C|1002 }C1 - 145
11X-RAY DIFFRACTION3{ C|1 - C|145 C|148 - C|154 C|158 - C|572 C|579 - C|609 C|1001 - C|1002 }C148 - 154
12X-RAY DIFFRACTION3{ C|1 - C|145 C|148 - C|154 C|158 - C|572 C|579 - C|609 C|1001 - C|1002 }C158 - 572
13X-RAY DIFFRACTION3{ C|1 - C|145 C|148 - C|154 C|158 - C|572 C|579 - C|609 C|1001 - C|1002 }C579 - 609
14X-RAY DIFFRACTION3{ C|1 - C|145 C|148 - C|154 C|158 - C|572 C|579 - C|609 C|1001 - C|1002 }C1001 - 1002
15X-RAY DIFFRACTION4{ D|1 - D|145 D|148 - D|154 D|159 - D|570 D|579 - D|614 D|1001 - D|1005 }D1 - 145
16X-RAY DIFFRACTION4{ D|1 - D|145 D|148 - D|154 D|159 - D|570 D|579 - D|614 D|1001 - D|1005 }D148 - 154
17X-RAY DIFFRACTION4{ D|1 - D|145 D|148 - D|154 D|159 - D|570 D|579 - D|614 D|1001 - D|1005 }D159 - 570
18X-RAY DIFFRACTION4{ D|1 - D|145 D|148 - D|154 D|159 - D|570 D|579 - D|614 D|1001 - D|1005 }D579 - 614
19X-RAY DIFFRACTION4{ D|1 - D|145 D|148 - D|154 D|159 - D|570 D|579 - D|614 D|1001 - D|1005 }D1001 - 1005
20X-RAY DIFFRACTION5{ E|1 - E|145 E|148 - E|154 E|159 - E|570 E|580 - E|608 E|1001 - E|1003 }E1 - 145
21X-RAY DIFFRACTION5{ E|1 - E|145 E|148 - E|154 E|159 - E|570 E|580 - E|608 E|1001 - E|1003 }E148 - 154
22X-RAY DIFFRACTION5{ E|1 - E|145 E|148 - E|154 E|159 - E|570 E|580 - E|608 E|1001 - E|1003 }E159 - 570
23X-RAY DIFFRACTION5{ E|1 - E|145 E|148 - E|154 E|159 - E|570 E|580 - E|608 E|1001 - E|1003 }E580 - 608
24X-RAY DIFFRACTION5{ E|1 - E|145 E|148 - E|154 E|159 - E|570 E|580 - E|608 E|1001 - E|1003 }E1001 - 1003
25X-RAY DIFFRACTION6{ F|1 - F|144 F|147 - F|154 F|159 - F|569 F|583 - F|610 F|1001 - F|1006 }F1 - 144
26X-RAY DIFFRACTION6{ F|1 - F|144 F|147 - F|154 F|159 - F|569 F|583 - F|610 F|1001 - F|1006 }F147 - 154
27X-RAY DIFFRACTION6{ F|1 - F|144 F|147 - F|154 F|159 - F|569 F|583 - F|610 F|1001 - F|1006 }F159 - 569
28X-RAY DIFFRACTION6{ F|1 - F|144 F|147 - F|154 F|159 - F|569 F|583 - F|610 F|1001 - F|1006 }F583 - 610
29X-RAY DIFFRACTION6{ F|1 - F|144 F|147 - F|154 F|159 - F|569 F|583 - F|610 F|1001 - F|1006 }F1001 - 1006
30X-RAY DIFFRACTION7{ G|3 - G|28 G|31 - G|54 }G3 - 28
31X-RAY DIFFRACTION7{ G|3 - G|28 G|31 - G|54 }G31 - 54
32X-RAY DIFFRACTION8{ H|2 - H|28 H|31 - H|54 }H2 - 28
33X-RAY DIFFRACTION8{ H|2 - H|28 H|31 - H|54 }H31 - 54
34X-RAY DIFFRACTION9{ I|3 - I|28 I|31 - I|54 }I3 - 28
35X-RAY DIFFRACTION9{ I|3 - I|28 I|31 - I|54 }I31 - 54
36X-RAY DIFFRACTION10{ J|2 - J|28 J|31 - J|54 }J2 - 28
37X-RAY DIFFRACTION10{ J|2 - J|28 J|31 - J|54 }J31 - 54
38X-RAY DIFFRACTION11{ K|3 - K|28 K|31 - K|53 }K3 - 28
39X-RAY DIFFRACTION11{ K|3 - K|28 K|31 - K|53 }K31 - 53
40X-RAY DIFFRACTION12{ L|2 - L|28 L|31 - L|54 }L2 - 28
41X-RAY DIFFRACTION12{ L|2 - L|28 L|31 - L|54 }L31 - 54

+
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://pdbjlvh1.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