[English] 日本語
Yorodumi
- PDB-5i5k: Structure of complement C5 in complex with eculizumab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5i5k
TitleStructure of complement C5 in complex with eculizumab
Components
  • Complement C5
  • Eculizumab heavy chain (variable domain)
  • Eculizumab light chain (variable domain)
KeywordsIMMUNE SYSTEM / Complement / Fab
Function / homology
Function and homology information


Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / positive regulation of chemokine production / Peptide ligand-binding receptors ...Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / positive regulation of chemokine production / Peptide ligand-binding receptors / complement activation, classical pathway / Regulation of Complement cascade / chemotaxis / G alpha (i) signalling events / killing of cells of another organism / cell surface receptor signaling pathway / inflammatory response / G protein-coupled receptor signaling pathway / signaling receptor binding / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
: / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. ...: / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsSchatz-Jakobsen, J.A. / Andersen, G.R.
CitationJournal: J Immunol. / Year: 2016
Title: Structural Basis for Eculizumab-Mediated Inhibition of the Complement Terminal Pathway.
Authors: Schatz-Jakobsen, J.A. / Zhang, Y. / Johnson, K. / Neill, A. / Sheridan, D. / Andersen, G.R.
History
DepositionFeb 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jun 29, 2016Group: Database references
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 / _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 2.1Jan 10, 2024Group: 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
B: Complement C5
H: Eculizumab heavy chain (variable domain)
L: Eculizumab light chain (variable domain)
A: Complement C5
X: Eculizumab heavy chain (variable domain)
Y: Eculizumab light chain (variable domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)474,2288
Polymers473,0556
Non-polymers1,1732
Water00
1
B: Complement C5
H: Eculizumab heavy chain (variable domain)
L: Eculizumab light chain (variable domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,1144
Polymers236,5283
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Complement C5
X: Eculizumab heavy chain (variable domain)
Y: Eculizumab light chain (variable domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,1144
Polymers236,5283
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)197.704, 269.321, 202.824
Angle α, β, γ (deg.)90.00, 98.58, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Complement C5 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 4


Mass: 188512.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01031
#2: Antibody Eculizumab heavy chain (variable domain)


Mass: 24860.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Eculizumab light chain (variable domain)


Mass: 23154.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.64 Å3/Da / Density % sol: 78.2 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Imidazole pH 6.2 4% v/v Tacsimate pH 7 8% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 4.2→49.8 Å / Num. obs: 76073 / % possible obs: 99.6 % / Redundancy: 4.9 % / Rsym value: 0.166 / Net I/σ(I): 6.28
Reflection shellHighest resolution: 4.2 Å / Redundancy: 5.01 % / Mean I/σ(I) obs: 1.29 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KMT, 3PVM

4kmt

3pvm


Resolution: 4.2→49.795 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2436 1865 2.45 %
Rwork0.2045 --
obs0.2055 76073 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.2→49.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32452 0 78 0 32530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00333282
X-RAY DIFFRACTIONf_angle_d0.64145218
X-RAY DIFFRACTIONf_dihedral_angle_d10.37420052
X-RAY DIFFRACTIONf_chiral_restr0.0455150
X-RAY DIFFRACTIONf_plane_restr0.0045738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2-4.31350.33581430.32015687X-RAY DIFFRACTION100
4.3135-4.44040.32921430.30735672X-RAY DIFFRACTION100
4.4404-4.58360.351430.28875704X-RAY DIFFRACTION100
4.5836-4.74730.34321440.27255714X-RAY DIFFRACTION100
4.7473-4.93720.32251430.26545696X-RAY DIFFRACTION99
4.9372-5.16170.28641420.23125653X-RAY DIFFRACTION100
5.1617-5.43350.26281440.22285714X-RAY DIFFRACTION100
5.4335-5.77340.28361440.22235722X-RAY DIFFRACTION100
5.7734-6.21840.27481430.21575715X-RAY DIFFRACTION100
6.2184-6.84280.23551440.20535701X-RAY DIFFRACTION100
6.8428-7.82970.25011450.18295746X-RAY DIFFRACTION100
7.8297-9.8520.17221430.15375719X-RAY DIFFRACTION100
9.852-49.79830.18741440.16165765X-RAY DIFFRACTION99
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)
11.88021.0083-1.27442.443-0.9291.1086-0.1122.0171-0.7777-0.98581.0143-0.9781.33722.66330.08931.5383-0.21390.03865.2491-0.42742.217846.419782.711834.6804
21.91921.08830.85553.04882.84183.685-0.59493.78880.02340.22920.8936-0.0874-0.46661.06740.00221.6432-0.25760.03763.2998-0.29531.81839.929172.842442.0811
31.2027-0.7604-1.84851.61251.75782.45150.01521.59540.9981-1.61760.17030.08330.4953-0.327702.663-0.8105-0.71043.46251.01462.2688-14.993693.18823.7668
40.2971-0.7745-0.27271.4510.75580.1456-0.72981.07111.047-1.54760.82080.3868-1.16970.08230.00042.9705-1.5073-0.53015.95181.39572.721419.5281103.44069.8054
52.3752-0.0012-1.76353.1961-0.55661.3745-1.58541.99561.8647-1.9620.82320.6276-0.81061.7126-0.33092.8808-1.73170.23157.12160.54332.08838.214688.079912.636
62.48692.00460.46262.38971.64061.1247-0.89170.8513-0.1413-0.53591.2697-0.44260.33220.953601.8436-0.17080.26323.5923-0.61631.71184.160863.075224.5316
72.6095-0.1065-1.10842.00321.02514.6689-0.4402-0.3016-1.2742-0.269-0.2035-0.02560.59471.6796-0.00052.1256-0.1146-0.26562.7797-0.03121.8026-30.22753.929925.4987
81.4337-1.72630.12511.8276-0.0896-0.0092-0.61183.82751.41830.01610.9499-0.0468-0.35571.08770.00222.6337-0.8450.00274.55610.55782.082324.967788.740627.1753
94.2044-0.3177-0.2361-0.05910.34043.01070.44390.8677-1.12010.0982-0.1239-0.18350.6679-0.09930.00022.4578-0.0708-0.01561.4266-0.03312.1414-19.065841.498165.9448
103.4033-1.72-1.39735.79020.09063.7375-0.03640.1247-0.00920.26970.0480.2402-0.04620.5210.00011.5394-0.1476-0.12931.3459-0.02021.3045-8.694767.664673.1274
114.250.740.60785.59822.50393.50090.34290.69330.39560.1995-0.29250.26540.41920.0907-01.7228-0.2001-0.07561.69160.14811.5093-33.366472.639554.7223
122.5171-2.3915-0.2732.24660.99551.17241.22242.73471.3379-0.9417-0.76850.0213-0.35060.61050.00072.16660.18620.17872.78120.65892.3987-26.383898.126646.7868
131.7035-0.5497-1.76710.11940.5371.56241.4306-0.9894-1.04442.49710.59370.9587-0.6265-1.6659-0.0024.1503-0.63530.02393.60080.27773.8026-56.216338.685653.3085
143.1274-1.26342.25632.7482-0.21463.518-0.1014-0.20640.1311-1.0776-0.2610.1102-0.37940.2102-0.00041.6361-0.0296-0.33962.1279-0.1082.108769.3023104.3467133.8584
150.02230.0396-0.12990.0888-0.32750.2969-1.1575-4.41481.88650.98670.3883-0.6587-2.0733-1.17760.00332.74130.5159-1.00624.9418-0.78613.329390.7756107.6213163.8024
160.7254-0.5561.14260.5326-0.74571.6232-0.5733-1.5528-0.2362-0.4150.4851-0.95271.39881.74160.00021.74850.3197-0.12082.47170.03582.859783.42987.9934131.1116
170.06470.15220.24331.21831.71082.2809-0.6429-1.56251.00632.7381-1.0630.53562.7427-2.5781-0.06393.16440.2456-0.22675.0468-0.14622.64790.009292.1838167.0681
182.37260.6547-1.83231.6911-1.25092.70050.26720.6053-0.2937-1.2958-0.5180.45680.88660.79610.00032.3748-0.12060.00281.4977-0.30911.678422.519635.282275.5519
194.7651-0.50580.13792.9564-0.24641.9839-0.1060.4396-0.0292-0.7254-0.2992-0.1209-0.0994-0.3508-01.6535-0.22130.1711.2054-0.05461.906932.2371.658483.1756
204.79661.6931-3.42792.265-0.56953.6283-0.41230.2514-0.22990.19520.3089-0.37470.25370.140501.59170.1967-0.12251.5892-0.07911.692828.057281.4136118.3565
212.5223-0.38160.03953.90921.7324.73020.0686-0.1356-0.1866-0.13790.1115-0.2669-0.37980.10480.00021.72790.02980.09151.30180.07411.685922.155842.8727116.6889
222.44930.2487-0.41584.7864-1.72332.75860.338-0.6589-0.0882-0.3345-0.4469-0.99060.81450.9286-0.00031.80980.10120.03960.9951-0.05531.947430.645930.627297.5595
233.69631.34731.73932.64390.49410.72890.3224-0.3549-0.66030.867-0.0698-0.41290.2315-0.04420.00011.56160.1749-0.04621.4840.00832.115350.328769.59793.3101
242.2873-1.83762.20446.2915-1.40462.08550.03-0.82590.1524-0.55580.7422-0.86840.403-0.0977-0.00051.6376-0.19850.04291.7122-0.10342.060862.1517101.1343106.0784
251.28451.2708-1.37361.4546-0.74081.60890.2134-0.0472-0.3157-0.5891-0.4822-0.9002-0.776-0.3658-0.0011.92870.08570.15991.6149-0.01781.893224.284249.380294.1844
261.1354-0.23581.09762.9790.53883.1052-0.43290.65680.0240.41020.19530.10540.1730.08310.00011.849-0.25470.39562.01690.082.150652.1106111.760164.8671
273.945-1.4879-0.19443.5846-0.10553.89110.06380.67330.5203-0.16480.15720.05520.1078-0.25420.00011.5923-0.1301-0.09111.45980.22821.578524.364103.283967.0735
284.43061.00741.26061.3470.81782.8279-0.2108-0.31340.49060.33630.04280.1954-0.2165-0.20.00011.7612-0.08830.05651.328-0.01312.021632.3065115.396594.6979
290.978-0.8665-0.43990.87770.09460.8999-0.8356-0.72620.19120.9949-0.1074-0.08450.4055-0.6575-0.00012.60680.01920.16212.10890.23652.41612.9786102.2486109.2576
303.03780.09290.00445.2699-1.94434.05070.15520.53690.3348-0.81230.5769-0.9104-0.54860.5409-0.00021.8211-0.07330.33941.2477-0.17532.256965.007140.484393.665
312.25841.88360.53921.6471-0.20142.79640.439-1.03340.73860.47560.84831.41141.4762-1.41620.00032.6896-0.5189-0.08933.1210.41091.9217-46.894457.83152.0379
320.8772-1.1434-0.05794.6151-0.25250.0148-0.151.6550.0522-2.2380.3429-0.2820.9325-4.30070.3822.9613-0.9709-0.81485.520.09081.8971-62.700950.8366-31.0962
332.6457-1.1444-1.42871.7758-1.07222.4139-0.52060.7581-0.51-2.37910.4469-0.0021.7571.5590.00092.9106-0.12950.0762.10790.05731.758-30.93148.0456-9.3747
344.62460.3699-0.13930.7338-0.44890.45970.23541.99052.2658-0.03330.24820.7851.8827-3.08830.06183.2691-0.3531-0.56334.82860.10761.3746-50.520657.4187-38.088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1resid 19:120 and chain a
2X-RAY DIFFRACTION2resid 121:224 and chain a
3X-RAY DIFFRACTION3resid 225:349 and chain a
4X-RAY DIFFRACTION4resid 350:460 and chain a
5X-RAY DIFFRACTION5resid 461:566 and chain a
6X-RAY DIFFRACTION6(resid 567:606 or resid 760:821) and chain a
7X-RAY DIFFRACTION7resid 822:930 and chain a
8X-RAY DIFFRACTION8resid 607:673 and chain a
9X-RAY DIFFRACTION9(resid 931:983 or resid 1305:1367) and chain a
10X-RAY DIFFRACTION10resid 984:1304 and chain a
11X-RAY DIFFRACTION11resid 1368:1520 and chain a
12X-RAY DIFFRACTION12resid 676:759 and chain a
13X-RAY DIFFRACTION13resid 1525:1700 and chain a
14X-RAY DIFFRACTION14chain h and resid 1:120
15X-RAY DIFFRACTION15chain h and resid 121:230
16X-RAY DIFFRACTION16chain l and resid 1:105
17X-RAY DIFFRACTION17chain l and resid 106:230
18X-RAY DIFFRACTION18resid 19:120 and chain b
19X-RAY DIFFRACTION19resid 121:224 and chain b
20X-RAY DIFFRACTION20resid 225:349 and chain b
21X-RAY DIFFRACTION21resid 350:460 and chain b
22X-RAY DIFFRACTION22resid 461:566 and chain b
23X-RAY DIFFRACTION23(resid 567:606 or resid 760:821) and chain b
24X-RAY DIFFRACTION24resid 822:930 and chain b
25X-RAY DIFFRACTION25resid 607:673 and chain b
26X-RAY DIFFRACTION26(resid 931:983 or resid 1305:1367) and chain b
27X-RAY DIFFRACTION27resid 984:1304 and chain B
28X-RAY DIFFRACTION28resid 1368:1520 and chain B
29X-RAY DIFFRACTION29resid 676:759 and chain B
30X-RAY DIFFRACTION30resid 1525:1700 and chain B
31X-RAY DIFFRACTION31chain X and resid 1:120
32X-RAY DIFFRACTION32chain X and resid 121:230
33X-RAY DIFFRACTION33chain Y and resid 1:105
34X-RAY DIFFRACTION34chain Y and resid 106:230

+
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