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- PDB-6onb: Crystal Structure of the ZIG-8-RIG-5 IG1-IG1 heterodimer, monocli... -

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Basic information

Entry
Database: PDB / ID: 6onb
TitleCrystal Structure of the ZIG-8-RIG-5 IG1-IG1 heterodimer, monoclinic form
Components
  • NeuRonal IgCAM-5
  • Zwei Ig domain protein zig-8
KeywordsCELL ADHESION / Cell surface receptor / Immunoglobulin superfamily / Nervous system / Heterodimer
Function / homology
Function and homology information


Degradation of the extracellular matrix / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / HS-GAG degradation / Integrin cell surface interactions / Laminin interactions / Non-integrin membrane-ECM interactions / ECM proteoglycans / neuron projection membrane / synapse organization ...Degradation of the extracellular matrix / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / HS-GAG degradation / Integrin cell surface interactions / Laminin interactions / Non-integrin membrane-ECM interactions / ECM proteoglycans / neuron projection membrane / synapse organization / neuron projection / extracellular region / membrane
Similarity search - Function
Zwei Ig domain protein zig-8 / : / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain ...Zwei Ig domain protein zig-8 / : / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig-like domain-containing protein / Zwei Ig domain protein zig-8
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.696 Å
AuthorsCheng, S. / Kurleto, J.D. / Ozkan, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS097161 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Family of neural wiring receptors in bilaterians defined by phylogenetic, biochemical, and structural evidence.
Authors: Cheng, S. / Park, Y. / Kurleto, J.D. / Jeon, M. / Zinn, K. / Thornton, J.W. / Ozkan, E.
History
DepositionApr 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _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.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 / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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 11, 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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zwei Ig domain protein zig-8
B: NeuRonal IgCAM-5
C: Zwei Ig domain protein zig-8
D: NeuRonal IgCAM-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,20811
Polymers55,0824
Non-polymers1,1267
Water7,278404
1
A: Zwei Ig domain protein zig-8
B: NeuRonal IgCAM-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3507
Polymers27,5412
Non-polymers8095
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-54 kcal/mol
Surface area12020 Å2
MethodPISA
2
C: Zwei Ig domain protein zig-8
D: NeuRonal IgCAM-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8584
Polymers27,5412
Non-polymers3172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-18 kcal/mol
Surface area11200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.460, 79.103, 89.977
Angle α, β, γ (deg.)90.00, 94.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Zwei Ig domain protein zig-8 / 2 Ig domain protein zig-8


Mass: 14297.955 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: zig-8, Y39E4B.8 / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G5ED00
#2: Protein NeuRonal IgCAM-5


Mass: 13242.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: rig-5, C36F7.4, CELE_C36F7.4 / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C6KRM7

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Sugars , 2 types, 2 molecules

#3: 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.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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.: 1 / Source method: isolated from a natural 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

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Non-polymers , 2 types, 409 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.87 Å3/Da / Density % sol: 57.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M lithium sulfate, 0.1 M sodium cacodylate, pH 6.5, 30% PEG 400

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 27, 2019
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.696→100 Å / Num. obs: 65564 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 34.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.055 / Net I/σ(I): 14.15
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 1.62 / Num. unique obs: 10243 / CC1/2: 0.812 / Rrim(I) all: 0.692 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHENIX1.15rc3_3435refinement
XDS20180808data reduction
PHASER2.8.3phasing
Cootmodel building
XDS20180808data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ON9

6on9


Resolution: 1.696→89.733 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.03
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 3179 4.85 %Random selection
Rwork0.1739 ---
obs0.1755 65514 96.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.696→89.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3491 0 67 404 3962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063705
X-RAY DIFFRACTIONf_angle_d0.8215066
X-RAY DIFFRACTIONf_dihedral_angle_d12.4372280
X-RAY DIFFRACTIONf_chiral_restr0.058582
X-RAY DIFFRACTIONf_plane_restr0.005664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6961-1.72140.4351190.42522380X-RAY DIFFRACTION85
1.7214-1.74830.3361510.33172698X-RAY DIFFRACTION97
1.7483-1.77690.34351360.31242724X-RAY DIFFRACTION97
1.7769-1.80760.34371330.28332664X-RAY DIFFRACTION96
1.8076-1.84050.27711430.22892686X-RAY DIFFRACTION95
1.8405-1.87590.21651480.19382673X-RAY DIFFRACTION98
1.8759-1.91420.22781360.18362731X-RAY DIFFRACTION98
1.9142-1.95580.19361150.18162749X-RAY DIFFRACTION98
1.9558-2.00130.1941470.18072727X-RAY DIFFRACTION98
2.0013-2.05130.21161380.18222727X-RAY DIFFRACTION98
2.0513-2.10680.23431490.17922741X-RAY DIFFRACTION98
2.1068-2.16880.2121570.1642653X-RAY DIFFRACTION96
2.1688-2.23880.20951310.16962672X-RAY DIFFRACTION95
2.2388-2.31880.20881180.16332767X-RAY DIFFRACTION98
2.3188-2.41170.2021190.17432754X-RAY DIFFRACTION98
2.4117-2.52140.21451370.16882764X-RAY DIFFRACTION99
2.5214-2.65440.22361210.17692791X-RAY DIFFRACTION98
2.6544-2.82070.18851530.17692670X-RAY DIFFRACTION95
2.8207-3.03850.20451380.17242723X-RAY DIFFRACTION98
3.0385-3.34430.1971280.16782792X-RAY DIFFRACTION99
3.3443-3.82820.18391660.162755X-RAY DIFFRACTION99
3.8282-4.82310.18541320.13872716X-RAY DIFFRACTION96
4.8231-89.85840.20841640.17982778X-RAY DIFFRACTION97
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)
12.294-1.46090.38074.3236-1.52973.06130.0051-0.08110.01720.1355-0.03560.28060.0369-0.12720.05110.21280.04460.01810.1713-0.05040.278916.13187.404740.1365
27.6373-0.8152.21582.0717-0.04084.8576-0.0989-0.01980.348-0.0212-0.0293-0.5063-0.50480.47010.03890.24150.00060.00740.1912-0.00870.279529.47984.37837.4609
30.86420.18360.91334.07491.08345.41370.08620.1604-0.0006-0.1452-0.0783-0.1221-0.05080.2640.03350.19240.03160.0140.1532-0.01710.212624.3391-5.87630.2663
42.87523.25424.84033.9185.60798.2353-0.52730.36630.1184-1.31840.3967-0.3982-1.11830.46120.01050.4209-0.01460.0790.2497-0.00880.334628.98114.818529.2522
54.0097-0.66961.63623.4043-0.13824.84260.01070.05570.0857-0.3196-0.07540.0466-0.1974-0.17740.10490.16610.05050.02270.1104-0.03070.171820.87423.325335.1136
60.7368-0.0474-0.30771.9512-2.71923.89040.1095-0.0129-0.0468-0.1152-0.03470.00560.6073-0.3497-0.13680.2458-0.0410.00130.19060.01070.273323.8681-24.870643.7031
71.12550.37990.65820.7694-0.86332.22940.09720.00360.0053-0.09050.06090.14870.0997-0.0359-0.11910.18770.01010.00950.15040.00450.227225.3478-17.66738.2414
82.6262-0.33932.24082.3926-1.98853.1178-0.07380.00250.14150.1305-0.0967-0.0095-0.21840.27710.14340.18210.00270.010.1351-0.02090.22833.9398-9.909343.7403
93.71442.47433.27638.53724.52183.76080.53160.6737-1.03870.35820.3177-0.99021.06360.6809-0.61780.29030.0504-0.02170.3304-0.12430.415634.3918-24.170937.6493
102.0170.52981.151.41551.8242.48880.15430.0773-0.3212-0.00160.0005-0.00250.4757-0.0962-0.06960.22110.0048-0.01640.1791-0.01690.263231.2813-21.762141.7947
113.5768-2.55512.68123.0073-0.03594.90820.1103-0.74410.73450.4899-0.1465-0.0607-0.3371-0.00370.06850.2746-0.07790.02160.2316-0.02510.303928.3079-15.269856.7527
121.33890.46510.93190.7752-0.42827.17280.16270.191-0.1347-0.14050.02430.18460.3032-0.0766-0.19320.20010.0127-0.01210.1672-0.01340.23220.5026-15.137136.2762
134.29660.23983.04342.25910.60612.26360.0468-0.812-0.0120.3076-0.20520.14720.7789-1.34160.16910.2515-0.050.00990.2707-0.00050.271720.9706-19.574651.4796
145.9740.86692.4481.95180.42412.5853-0.00411.2229-0.6642-0.7487-0.0887-0.5080.82791.30890.12090.60210.1910.12220.8782-0.12480.402136.4024-19.4619-2.7091
151.04171.0469-0.86813.26563.3688.84110.4320.135-0.52750.21660.1775-0.61420.99861.5552-0.56380.32160.2206-0.02590.8229-0.03840.390643.6966-18.225814.8108
164.53690.6646-0.92345.6259-1.65855.86010.18140.76380.9887-0.7308-0.1940.0761-0.39370.7621-0.00250.4390.00720.03590.48450.14550.399433.3282-6.7213.2426
173.65381.3456-0.74640.4872-0.27575.9692-0.02110.05690.1821-0.10720.02360.0276-0.11490.1093-0.02580.2370.04740.0150.21450.00580.188226.3372-11.211213.4211
187.82895.109-6.13794.5638-5.89227.60690.4981-0.22450.8764-0.2273-0.18230.0246-0.95610.8221-0.23540.5534-0.05750.1160.42680.04870.402536.206-3.80168.6351
194.71850.41930.45874.24640.50975.37690.050.307-0.1061-0.22610.0462-0.07760.29720.7797-0.04250.28040.09430.0750.4116-0.0210.235234.3814-14.38947.33
208.00972.41382.90727.17450.38671.09550.3112-0.3304-0.1213-0.0249-0.48620.39360.8097-1.85310.16810.2983-0.0718-0.0710.5587-0.02240.2778.9062-17.306120.4246
211.02970.35310.97961.07930.85122.8310.10080.2185-0.0262-0.286-0.19520.20970.0657-0.7360.08610.3340.0668-0.06620.5135-0.05930.27059.9354-15.4655.0322
223.51871.32032.31373.1268-0.96532.77210.06360.92230.5134-0.7468-0.1366-0.0361-0.5358-0.23260.18470.45420.1216-0.05440.46630.05630.284717.3896-6.72531.068
233.4750.28210.2165.20310.53794.6789-0.1298-0.01250.7385-0.1587-0.11180.4523-0.9177-1.12990.20540.42070.1803-0.13350.5823-0.06890.3746.1209-7.45798.0404
247.333-0.42130.44298.5237-1.88436.4347-0.25291.16920.1203-1.5440.4343-0.0948-0.43890.1511-0.13250.67530.083-0.11110.8429-0.02740.273110.8569-15.0633-10.2004
252.05580.21032.7090.7661.04138.23190.24080.0555-0.1881-0.2114-0.0890.13920.2913-0.5732-0.14720.27010.0305-0.03120.3543-0.01920.22416.9707-17.75910.7784
265.27170.01764.62131.2914-0.4524.20630.30190.5846-0.4047-0.3324-0.4119-0.09890.7849-0.42680.04130.47280.0785-0.10250.6025-0.1420.3349.7258-21.5534-1.2543
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 71 )
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 90 )
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 97 )
5X-RAY DIFFRACTION5chain 'A' and (resid 98 through 137 )
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 41 )
7X-RAY DIFFRACTION7chain 'B' and (resid 42 through 65 )
8X-RAY DIFFRACTION8chain 'B' and (resid 66 through 80 )
9X-RAY DIFFRACTION9chain 'B' and (resid 81 through 92 )
10X-RAY DIFFRACTION10chain 'B' and (resid 93 through 98 )
11X-RAY DIFFRACTION11chain 'B' and (resid 99 through 106 )
12X-RAY DIFFRACTION12chain 'B' and (resid 107 through 118 )
13X-RAY DIFFRACTION13chain 'B' and (resid 119 through 130 )
14X-RAY DIFFRACTION14chain 'C' and (resid 23 through 43 )
15X-RAY DIFFRACTION15chain 'C' and (resid 44 through 52 )
16X-RAY DIFFRACTION16chain 'C' and (resid 53 through 71 )
17X-RAY DIFFRACTION17chain 'C' and (resid 72 through 90 )
18X-RAY DIFFRACTION18chain 'C' and (resid 91 through 99 )
19X-RAY DIFFRACTION19chain 'C' and (resid 100 through 136 )
20X-RAY DIFFRACTION20chain 'D' and (resid 21 through 27 )
21X-RAY DIFFRACTION21chain 'D' and (resid 28 through 65 )
22X-RAY DIFFRACTION22chain 'D' and (resid 66 through 80 )
23X-RAY DIFFRACTION23chain 'D' and (resid 81 through 98 )
24X-RAY DIFFRACTION24chain 'D' and (resid 99 through 106 )
25X-RAY DIFFRACTION25chain 'D' and (resid 107 through 118 )
26X-RAY DIFFRACTION26chain 'D' and (resid 119 through 129 )

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  • 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

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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

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