[English] 日本語
Yorodumi
- PDB-5uk5: Complex of Notch1(EGF8-12) bound to Jagged1(N-EGF3) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uk5
TitleComplex of Notch1(EGF8-12) bound to Jagged1(N-EGF3)
Components
  • Neurogenic locus notch homolog protein 1
  • Protein jagged-1
KeywordsSIGNALING PROTEIN / Notch / Jagged / Delta / Glycoprotein
Function / homology
Function and homology information


Notch signaling involved in heart development / NOTCH3 Activation and Transmission of Signal to the Nucleus / endocardial cushion cell development / loop of Henle development / ciliary body morphogenesis / regulation of cardioblast proliferation / regulation of inner ear auditory receptor cell differentiation / pulmonary artery morphogenesis / cardiac neural crest cell development involved in outflow tract morphogenesis / positive regulation of glial cell differentiation ...Notch signaling involved in heart development / NOTCH3 Activation and Transmission of Signal to the Nucleus / endocardial cushion cell development / loop of Henle development / ciliary body morphogenesis / regulation of cardioblast proliferation / regulation of inner ear auditory receptor cell differentiation / pulmonary artery morphogenesis / cardiac neural crest cell development involved in outflow tract morphogenesis / positive regulation of glial cell differentiation / podocyte development / negative regulation of endothelial cell differentiation / venous blood vessel morphogenesis / morphogenesis of an epithelial sheet / nephron development / positive regulation of myeloid cell differentiation / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis / cardiac right ventricle formation / growth involved in heart morphogenesis / Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation / cell differentiation in spinal cord / retinal cone cell differentiation / venous endothelial cell differentiation / arterial endothelial cell differentiation / cardiac chamber formation / epithelial cell fate commitment / negative regulation of pro-B cell differentiation / negative regulation of inner ear auditory receptor cell differentiation / mitral valve formation / cardiac right ventricle morphogenesis / cell migration involved in endocardial cushion formation / glomerular mesangial cell development / negative regulation of photoreceptor cell differentiation / negative regulation of cell proliferation involved in heart valve morphogenesis / regulation of somitogenesis / inhibition of neuroepithelial cell differentiation / endocardium morphogenesis / atrioventricular node development / foregut morphogenesis / regulation of cell adhesion involved in heart morphogenesis / distal tubule development / MAML1-RBP-Jkappa- ICN1 complex / regulation of epithelial cell proliferation involved in prostate gland development / auditory receptor cell fate commitment / positive regulation of aorta morphogenesis / negative regulation of endothelial cell chemotaxis / neuroendocrine cell differentiation / collecting duct development / negative regulation of extracellular matrix constituent secretion / positive regulation of transcription of Notch receptor target / positive regulation of smooth muscle cell differentiation / cellular response to tumor cell / positive regulation of viral transcription / positive regulation of apoptotic process involved in morphogenesis / compartment pattern specification / vasculogenesis involved in coronary vascular morphogenesis / aorta morphogenesis / T-helper 17 type immune response / endocardial cushion development / epithelial to mesenchymal transition involved in endocardial cushion formation / regulation of extracellular matrix assembly / endocardial cell differentiation / cardiac ventricle morphogenesis / T cell mediated immunity / cardiac left ventricle morphogenesis / mesenchymal cell development / epidermal cell fate specification / regulation of Notch signaling pathway / negative regulation of collagen biosynthetic process / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / negative regulation of myotube differentiation / somatic stem cell division / left/right axis specification / negative regulation of cell adhesion molecule production / negative regulation of cardiac muscle hypertrophy / positive regulation of endothelial cell differentiation / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / interleukin-17-mediated signaling pathway / apoptotic process involved in embryonic digit morphogenesis / endocardium development / glial cell differentiation / positive regulation of cardiac epithelial to mesenchymal transition / inner ear auditory receptor cell differentiation / cardiac epithelial to mesenchymal transition / negative regulation of calcium ion-dependent exocytosis / neuron fate commitment / cardiac muscle cell myoblast differentiation / cellular response to follicle-stimulating hormone stimulus / pericardium morphogenesis / cardiac atrium morphogenesis / negative regulation of catalytic activity / tissue regeneration / neuronal stem cell population maintenance / tube formation / positive regulation of astrocyte differentiation / negative regulation of oligodendrocyte differentiation / endoderm development / regulation of stem cell proliferation
Similarity search - Function
Jagged/Serrate protein / Delta/Serrate/lag-2 (DSL) protein / Notch ligand, N-terminal domain / Delta serrate ligand / N terminus of Notch ligand C2-like domain / DSL domain profile. / delta serrate ligand / Neurogenic locus notch homolog protein 1 / Notch, C-terminal / Domain of unknown function ...Jagged/Serrate protein / Delta/Serrate/lag-2 (DSL) protein / Notch ligand, N-terminal domain / Delta serrate ligand / N terminus of Notch ligand C2-like domain / DSL domain profile. / delta serrate ligand / Neurogenic locus notch homolog protein 1 / Notch, C-terminal / Domain of unknown function / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein / NOD / NODP / Notch-like domain superfamily / LNR (Lin-12/Notch) repeat profile. / LNR domain / Notch domain / Domain found in Notch and Lin-12 / von Willebrand factor (vWF) type C domain / EGF-like, conserved site / Human growth factor-like EGF / von Willebrand factor (vWF) type C domain / VWFC domain / Calcium-binding EGF domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Ankyrin repeat / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
beta-D-glucopyranose / alpha-L-fucopyranose / Neurogenic locus notch homolog protein 1 / Protein jagged-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.506 Å
AuthorsGarcia, K.C. / Luca, V.C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH-1R01-GM097015 United States
Howard Hughes Medical Institute (HHMI) United States
Ludwig Cancer Foundation United States
CitationJournal: Science / Year: 2017
Title: Notch-Jagged complex structure implicates a catch bond in tuning ligand sensitivity.
Authors: Luca, V.C. / Kim, B.C. / Ge, C. / Kakuda, S. / Wu, D. / Roein-Peikar, M. / Haltiwanger, R.S. / Zhu, C. / Ha, T. / Garcia, K.C.
History
DepositionJan 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Apr 12, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Nov 20, 2019Group: 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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neurogenic locus notch homolog protein 1
B: Protein jagged-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,43314
Polymers57,5102
Non-polymers1,92312
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint5 kcal/mol
Surface area29450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.457, 127.995, 154.288
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Neurogenic locus notch homolog protein 1 / Notch 1


Mass: 21777.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Notch1 / Plasmid: pAcGp67A / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q07008
#2: Protein Protein jagged-1 / Jagged1


Mass: 35733.000 Da / Num. of mol.: 1 / Mutation: S32L, R68G, D72N, T87R, Q182R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Jag1 / Plasmid: pAcGp67A / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q63722

-
Sugars , 4 types, 8 molecules

#3: Polysaccharide alpha-D-xylopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 312.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-3DGlcpb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a212h-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][b-D-Glcp]{[(3+1)][a-D-Xylp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: 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.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 142 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.6
Details: 22.5% PEG 1000, 0.1 M MES pH 6.6, 3% dextran sulfate Mr(5000)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 15, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 23570 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 62 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.041 / Rrim(I) all: 0.097 / Χ2: 1.042 / Net I/σ(I): 7.9 / Num. measured all: 175202
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.5-2.597.521920.7340.6081.021100
2.59-2.697.50.7830.4371.077100
2.69-2.827.50.8890.2861.0711000.7330.787
2.82-2.967.50.9480.1981.061000.5060.544
2.96-3.157.50.9780.1161.0811000.2970.319
3.15-3.397.50.9890.0691.0081000.1750.188
3.39-3.737.50.9940.0461.0621000.1180.126
3.73-4.277.40.9960.0311.081000.080.086
4.27-5.387.40.9970.0231.0231000.0590.064
5.38-507.10.9970.0210.93599.60.0520.056

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CC0, 4XL1

4cc0

4xl1


Resolution: 2.506→44.741 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.7
RfactorNum. reflection% reflection
Rfree0.2625 1178 5 %
Rwork0.219 --
obs0.2211 23544 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.506→44.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3780 0 115 138 4033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074021
X-RAY DIFFRACTIONf_angle_d0.865485
X-RAY DIFFRACTIONf_dihedral_angle_d12.3091516
X-RAY DIFFRACTIONf_chiral_restr0.049565
X-RAY DIFFRACTIONf_plane_restr0.004726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5062-2.62030.39111370.33222618X-RAY DIFFRACTION95
2.6203-2.75840.37191470.29392789X-RAY DIFFRACTION100
2.7584-2.93120.34231460.28922763X-RAY DIFFRACTION100
2.9312-3.15750.33131470.27782788X-RAY DIFFRACTION100
3.1575-3.47510.2951470.25012792X-RAY DIFFRACTION100
3.4751-3.97770.2851480.20552817X-RAY DIFFRACTION100
3.9777-5.01040.21061510.1752848X-RAY DIFFRACTION100
5.0104-44.74850.22461550.20352951X-RAY DIFFRACTION100
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)
18.21087.47366.29346.8625.75087.6319-0.29860.29351.10341.7877-0.23510.3075-1.13022.30470.44611.8405-0.61080.01591.29850.00281.00872.672244.7419-34.6581
22.09057.97872.85048.9463-2.06514.3628-0.3225-3.08890.71110.2679-0.90791.4355-0.6497-0.37841.22581.9562-0.48620.49771.2132-0.58251.2424-16.083635.8502-32.1129
36.454.88513.96232.26319.9489.04041.0186-1.27710.20542.2619-1.67140.61431.0941-1.5160.53521.4373-0.4060.16691.0791-0.37321.3278-25.789816.9034-40.922
44.8578-6.9386-1.43558.7380.89370.89790.0068-0.38610.44821.2147-0.12810.43710.239-0.240.10690.7492-0.28810.01490.6922-0.21220.8161-27.3687-18.3619-57.3563
55.39481.8895-1.4542.0981-0.46414.56550.3382-0.795-1.33050.476-0.23751.04250.2344-0.2459-0.05380.8397-0.3191-0.19980.75750.18770.8855-24.0466-53.2565-55.1304
64.4191-0.2187-2.05875.70884.30229.16380.28420.5306-1.6227-0.3463-0.37-0.05250.86670.76890.19160.83810.1546-0.450.68590.01751.0924-3.5847-61.7017-80.9955
73.40650.8051-1.03784.81372.48515.7402-0.1248-0.1071-1.45910.4848-0.692-0.54630.61630.58150.58350.61570.0665-0.29980.56680.15480.964-6.3162-63.671-77.521
85.9671-3.2112-4.43855.89583.32596.24660.6859-0.0404-0.4034-0.3851-0.6463-0.4111-0.56670.0951-0.11870.5823-0.0812-0.33970.4640.08180.6577-8.4277-51.8124-76.0272
95.24110.7171.2457.83884.62397.51140.462-0.3651-0.95420.1978-0.3829-1.20530.60080.36060.0110.6534-0.0209-0.3390.50730.25420.92-5.4186-59.1354-74.7913
107.162-2.8665-3.52999.62256.7856.27450.5558-0.7507-0.00390.2467-0.4072-0.061-0.20210.4567-0.28840.6101-0.2064-0.17940.53260.06590.4596-8.1048-39.8933-67.7438
110.3959-0.43461.60168.56122.89375.00890.3339-0.48120.55430.22660.1728-0.8925-0.45560.5027-0.46360.6003-0.27690.13330.6406-0.1840.8194-10.1668-12.7986-58.2213
124.5477-3.1564-2.14729.93885.6245.27290.0806-0.39480.31610.6507-0.2386-0.8208-0.1828-0.22360.18051.042-0.1750.15650.554-0.22090.9218-12.659713.0001-50.6244
138.91571.2785-0.23489.7856-3.32018.1566-0.43990.75431.01491.4745-0.17910.351-0.87830.14210.60721.0181-0.1191-0.04470.6122-0.06040.9005-8.135547.2818-47.1033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 299:327))
2X-RAY DIFFRACTION2chain 'A' and (resid 328 through 347 )
3X-RAY DIFFRACTION3chain 'A' and (resid 348 through 399 )
4X-RAY DIFFRACTION4chain 'A' and (resid 400 through 454 )
5X-RAY DIFFRACTION5chain 'A' and (resid 455 through 493 )
6X-RAY DIFFRACTION6chain 'B' and (resid 28 through 63 )
7X-RAY DIFFRACTION7chain 'B' and (resid 64 through 85 )
8X-RAY DIFFRACTION8chain 'B' and (resid 86 through 130 )
9X-RAY DIFFRACTION9chain 'B' and (resid 131 through 177 )
10X-RAY DIFFRACTION10chain 'B' and (resid 178 through 202 )
11X-RAY DIFFRACTION11chain 'B' and (resid 203 through 242 )
12X-RAY DIFFRACTION12chain 'B' and (resid 243 through 283 )
13X-RAY DIFFRACTION13chain 'B' and (resid 284 through 335 )

+
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