[English] 日本語
Yorodumi
- PDB-8a0y: Crystal structure of mouse contactin 2 immunoglobulin domains -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a0y
TitleCrystal structure of mouse contactin 2 immunoglobulin domains
ComponentsContactin-2
KeywordsCELL ADHESION / cell adhesion molecule(s) / immunoglobulin / glycoprotein / myelin / juxtaparanodal / contactin / TAG-1 / axonin-1 / TAX-1 / horseshoe
Function / homology
Function and homology information


: / : / regulation of axon diameter / Signaling by ROBO receptors / establishment of protein localization to juxtaparanode region of axon / presynaptic membrane organization / positive regulation of adenosine receptor signaling pathway / regulation of astrocyte differentiation / clustering of voltage-gated potassium channels / cerebral cortex GABAergic interneuron migration ...: / : / regulation of axon diameter / Signaling by ROBO receptors / establishment of protein localization to juxtaparanode region of axon / presynaptic membrane organization / positive regulation of adenosine receptor signaling pathway / regulation of astrocyte differentiation / clustering of voltage-gated potassium channels / cerebral cortex GABAergic interneuron migration / protein localization to juxtaparanode region of axon / central nervous system myelination / positive regulation of protein processing / node of Ranvier / juxtaparanode region of axon / adult walking behavior / axonal fasciculation / regulation of neuronal synaptic plasticity / negative regulation of neuron differentiation / axonogenesis / cell-matrix adhesion / learning / axon guidance / neuron migration / receptor internalization / microtubule cytoskeleton organization / : / neuron projection development / myelin sheath / carbohydrate binding / neuron projection / axon / neuronal cell body / synapse / cell surface / plasma membrane
Similarity search - Function
Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype ...Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsChataigner, L.M.P. / Janssen, B.J.C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Structure / Year: 2024
Title: Contactin 2 homophilic adhesion structure and conformational plasticity.
Authors: Chataigner, L.M.P. / Tharichen, L. / Beugelink, J.W. / Granneman, J.C.M. / Mokiem, N.J. / Snijder, J. / Forster, F. / Janssen, B.J.C.
History
DepositionMay 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Contactin-2
B: Contactin-2
C: Contactin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,96722
Polymers193,6523
Non-polymers9,31619
Water00
1
A: Contactin-2
B: Contactin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,50715
Polymers129,1012
Non-polymers6,40613
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Contactin-2
C: Contactin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,08314
Polymers129,1012
Non-polymers5,98112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.930, 159.784, 227.886
Angle α, β, γ (deg.)90.000, 96.740, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 35 through 608 or resid 609...
21(chain B and (resid 35 through 608 or resid 609...
31(chain C and (resid 35 through 608 or resid 609...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 35 through 608 or resid 609...A35 - 608
121(chain A and (resid 35 through 608 or resid 609...A609 - 611
131(chain A and (resid 35 through 608 or resid 609...A613 - 615
141(chain A and (resid 35 through 608 or resid 609...A617
151(chain A and (resid 35 through 608 or resid 609...A623
211(chain B and (resid 35 through 608 or resid 609...B35 - 608
221(chain B and (resid 35 through 608 or resid 609...B609 - 611
231(chain B and (resid 35 through 608 or resid 609...B613 - 615
241(chain B and (resid 35 through 608 or resid 609...B617
251(chain B and (resid 35 through 608 or resid 609...B623
311(chain C and (resid 35 through 608 or resid 609...C35 - 608
321(chain C and (resid 35 through 608 or resid 609...C609 - 611
331(chain C and (resid 35 through 608 or resid 609...C613 - 615
341(chain C and (resid 35 through 608 or resid 609...C617
351(chain C and (resid 35 through 608 or resid 609...C623

NCS oper:
IDCodeMatrixVector
1given(0.764360448589, -0.594075450074, -0.250654072882), (-0.549431242796, -0.803542825311, 0.229007068299), (-0.33745875907, -0.0373267666797, -0.940599967264)-15.9000975859, -87.9139842871, 58.2224572695
2given(0.196612186868, 0.97045919897, -0.139830580021), (0.970754629421, -0.212710282389, -0.111309412106), (-0.137764645073, -0.113856395957, -0.983899193854)-34.241181827, 62.3649049464, 140.294744738

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Contactin-2 / Axonal glycoprotein TAG-1 / Axonin-1 / Transient axonal glycoprotein 1 / TAX-1


Mass: 64550.617 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cntn2, Tax / Production host: Homo sapiens (human) / References: UniProt: Q61330

-
Sugars , 7 types, 19 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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.: 2
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
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: 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.: 9 / 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

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.16 Å3/Da / Density % sol: 80.03 %
Crystal growTemperature: 269.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M Sodium malonate pH 6.0 and 12% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.5→65 Å / Num. obs: 58926 / % possible obs: 99.3 % / Redundancy: 6 % / CC1/2: 0.974 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.071 / Rrim(I) all: 0.175 / Net I/σ(I): 4.6 / Num. measured all: 351683 / Scaling rejects: 526
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.5-3.596.12.5482763444980.2381.1312.7930.598.5
15.24-655.80.11842787390.9660.0560.13114.197.7

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OM5

2om5


Resolution: 3.5→59.82 Å / SU ML: 0.63 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2643 2977 5.07 %
Rwork0.225 55772 -
obs0.227 58749 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 575.8 Å2 / Biso mean: 251.6085 Å2 / Biso min: 85.8 Å2
Refinement stepCycle: final / Resolution: 3.5→59.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13275 0 615 0 13890
Biso mean--262.46 --
Num. residues----1722
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8118X-RAY DIFFRACTION12.179TORSIONAL
12B8118X-RAY DIFFRACTION12.179TORSIONAL
13C8118X-RAY DIFFRACTION12.179TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.560.37871530.39822589274297
3.56-3.620.41431470.36542606275399
3.62-3.680.36641370.350927102847100
3.68-3.760.40741290.329126112740100
3.76-3.830.36831450.303726832828100
3.83-3.920.34221460.283826272773100
3.92-4.010.27911410.266427122853100
4.01-4.110.3211540.254126372791100
4.11-4.220.29521420.24672629277199
4.22-4.340.25831330.22782587272096
4.34-4.480.25581270.20382652277999
4.48-4.640.24781680.186526422810100
4.64-4.830.22811320.190726892821100
4.83-5.050.25251510.190426572808100
5.05-5.310.23131310.188626842815100
5.31-5.650.2451270.190126882815100
5.65-6.080.3281300.2052691282199
6.08-6.690.26361470.23442583273097
6.69-7.660.27941440.231826922836100
7.66-9.640.25281530.209426972850100
9.64-59.820.22811400.22332706284698
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)
19.3842-1.16492.56517.09832.01654.01450.03450.8972-0.1544-0.26760.8376-1.3033-0.7296-0.2578-0.81311.62380.1906-0.25621.60060.14772.7816-44.4551-48.122824.4935
25.6942-2.35932.01268.7541-4.38949.48210.3679-0.78720.82592.20450.2055-0.55370.55440.311-0.5671.89160.1986-0.50171.5591-0.23242.5434-6.8578-47.690843.6883
38.95953.63274.50823.77131.48149.4037-0.39321.3595-1.50790.58541.0967-1.94050.38550.9676-0.98212.01080.2574-0.83051.3873-0.46122.4428-7.3332-68.961236.5066
46.0387-1.7329-0.24327.27536.76157.63560.0503-0.09650.85190.2975-0.11950.0346-0.4204-0.1803-0.04481.1860.0803-0.33411.17780.05632.1626-50.7536-71.318222.0835
58.9871-3.1461-2.37558.4016-2.21029.06160.3443-0.3115-0.0399-0.9510.2127-0.19591.1581-0.3473-0.58660.82040.089-0.22981.18220.31621.1582-90.0567-76.3894-0.5616
67.54011.33931.95321.872-2.45827.92750.12991.12330.9520.07310.112-0.60981.09570.89320.24741.81960.1081-0.90661.498-0.36032.0368-97.5583-97.6998-31.4716
78.0231-1.5844-1.49388.0911.31179.2830.12831.1996-1.61730.1903-1.93542.44641.2013-1.67061.98111.7629-0.01340.24711.511-0.21472.1577-63.526325.504599.6521
810.02797.10747.75678.78433.81229.82280.2993-1.12640.62750.91-0.26440.6523-0.19910.4312-0.17181.3216-0.14940.13371.5191-0.16361.7641-70.246660.6772121.9899
95.43321.83522.14527.79590.32281.13160.82991.13760.993-2.02350.4126-1.1312-0.35711.1340.85660.9025-0.63910.55971.8468-0.29951.7272-50.556665.7683112.2498
104.0611-3.2592-0.79635.9503-2.6758.47280.35330.4620.0220.22610.6791-1.87871.88521.9944-0.41861.27430.6018-0.0832.05550.02121.3136-39.450724.925596.7024
111.7093-2.87691.40587.97320.25125.097-1.1139-0.7409-1.08561.51671.71161.12230.65441.61984.07451.90090.7318-0.22472.2422-0.44660.3507-17.90041.357369.6981
124.8353-3.8549-6.87434.55275.91199.31130.9775-1.36432.6919-0.7017-1.8013-1.3415-2.2219-1.54451.31143.6331-0.63320.03332.828-0.5084.2452-1.851424.816745.2823
137.6148-5.9922-7.58615.40995.53918.7205-1.517-0.7086-2.20320.3422-0.52792.21521.1779-2.0283-2.04010.94440.1895-0.67362.0307-0.78632.3041-36.1437-15.815148.2502
147.1279-0.87150.9084.27340.60654.15820.11852.09570.0409-1.5630.0149-0.1077-1.6837-0.22210.28631.36590.3052-0.58990.5236-0.29291.1252-6.7615-32.367223.394
154.0077-4.2705-4.6964.53684.17687.22490.7053-1.78380.54941.49380.1224-0.6879-1.88010.9596-0.81052.1729-0.64810.27591.6579-0.10722.0743.5573-13.17229.1692
164.4115-3.2099-1.42068.99071.0570.46270.58081.121.1598-2.863-0.4075-1.0053-0.8812-1.5017-0.97493.47611.1709-0.6181.9767-0.27631.7856-31.22828.21747.8235
176.7635-0.73883.93080.8176-1.75795.1751.42740.7404-1.5667-1.8776-1.22361.0517-0.4473-0.3939-0.45392.58010.6837-0.23331.7401-0.36990.5677-46.277337.087473.9571
180.49230.0743-0.39686.12642.97561.8187-0.7065-0.9399-1.4392.25070.7283-3.24830.90872.5010.08292.0429-0.52840.41343.5027-0.4883.5971-17.234250.585694.0206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'B' and ((resid 35 through 131) or (resid 609-612)))B0
2X-RAY DIFFRACTION2(chain 'B' and ((resid 132 through 235) or (resid 613-615)))B0
3X-RAY DIFFRACTION3(chain 'B' and resid 236 through 325)B236 - 325
4X-RAY DIFFRACTION4(chain 'B' and resid 326 through 416)B326 - 416
5X-RAY DIFFRACTION5(chain 'B' and ((resid 417 through 508) or (resid 616-624)))B0
6X-RAY DIFFRACTION6(chain 'B' and ((resid 509 through 608) or (resid 625)))B0
7X-RAY DIFFRACTION7(chain 'C' and ((resid 35 through 131) or (resid 609-611)))C0
8X-RAY DIFFRACTION8(chain 'C' and ((resid 132 through 235) or (resid 612-614)))C0
9X-RAY DIFFRACTION9(chain 'C' and resid 236 through 325)C236 - 325
10X-RAY DIFFRACTION10(chain 'C' and resid 326 through 416)C326 - 416
11X-RAY DIFFRACTION11(chain 'C' and ((resid 417 through 508) or (resid 615-623)))C0
12X-RAY DIFFRACTION12(chain 'C' and resid 509 through 608)C509 - 608
13X-RAY DIFFRACTION13(chain 'A' and ((resid 35 through 131) or (resid 609-612)))A0
14X-RAY DIFFRACTION14(chain 'A' and ((resid 132 through 235) or (resid 613-616)))A0
15X-RAY DIFFRACTION15(chain 'A' and resid 236 through 325)A236 - 325
16X-RAY DIFFRACTION16(chain 'A' and resid 326 through 416)A326 - 416
17X-RAY DIFFRACTION17(chain 'A' and ((resid 417 through 508) or (resid 617-624)))A0
18X-RAY DIFFRACTION18(chain 'A' and resid 509 through 608)A509 - 608

+
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