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- PDB-5edv: Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex -

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Basic information

Entry
Database: PDB / ID: 5edv
TitleStructure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex
Components
  • E3 ubiquitin-protein ligase RNF31
  • Polyubiquitin-B
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsLIGASE/TRANSFERASE / LUBAC / RBR / E3 ubiquitin ligase / E2 / LIGASE-TRANSFERASE complex
Function / homology
Function and homology information


protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / RBR-type E3 ubiquitin transferase / CD40 signaling pathway / positive regulation of xenophagy / CD40 receptor complex / (E3-independent) E2 ubiquitin-conjugating enzyme / negative regulation of necroptotic process / symbiont entry into host cell via disruption of host cell glycocalyx ...protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / RBR-type E3 ubiquitin transferase / CD40 signaling pathway / positive regulation of xenophagy / CD40 receptor complex / (E3-independent) E2 ubiquitin-conjugating enzyme / negative regulation of necroptotic process / symbiont entry into host cell via disruption of host cell glycocalyx / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / K48-linked polyubiquitin modification-dependent protein binding / K63-linked polyubiquitin modification-dependent protein binding / E2 ubiquitin-conjugating enzyme / symbiont entry into host cell via disruption of host cell envelope / virus tail / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / TNFR1-induced NF-kappa-B signaling pathway / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / ubiquitin binding / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CLEC7A (Dectin-1) signaling / positive regulation of NF-kappaB transcription factor activity / FCERI mediated NF-kB activation / protein modification process / cytoplasmic side of plasma membrane / protein polyubiquitination / ubiquitin-protein transferase activity / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin protein ligase activity / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / T cell receptor signaling pathway / ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination / defense response to bacterium / ubiquitin protein ligase binding / protein-containing complex / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase RNF31, UBA domain / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / : / : / : / : / : ...E3 ubiquitin-protein ligase RNF31, UBA domain / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / : / : / : / : / : / HOIP UBA domain pair / E3 Ubiquitin Ligase RBR C-terminal domain / PNGase/UBA- or UBX-containing domain / IBR domain, a half RING-finger domain / PUB domain / PUB-like domain superfamily / PUB domain / IBR domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ubiquitin family / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Tail fiber / Ubiquitin-conjugating enzyme E2 D2 / E3 ubiquitin-protein ligase RNF31
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.48 Å
AuthorsLechtenberg, B.C. / Mace, P.D. / Sanishvili, R. / Riedl, S.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)R01AA017238 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)ACB-12002 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AGM-12006 United States
CitationJournal: Nature / Year: 2016
Title: Structure of a HOIP/E2~ubiquitin complex reveals RBR E3 ligase mechanism and regulation.
Authors: Lechtenberg, B.C. / Rajput, A. / Sanishvili, R. / Dobaczewska, M.K. / Ware, C.F. / Mace, P.D. / Riedl, S.J.
History
DepositionOct 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Derived calculations
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.6Nov 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: E3 ubiquitin-protein ligase RNF31
B: E3 ubiquitin-protein ligase RNF31
C: Ubiquitin-conjugating enzyme E2 D2
D: Ubiquitin-conjugating enzyme E2 D2
E: Polyubiquitin-B
F: Polyubiquitin-B
G: Polyubiquitin-B
H: Polyubiquitin-B
I: Ubiquitin-conjugating enzyme E2 D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,20525
Polymers172,1599
Non-polymers1,04716
Water00
1
A: E3 ubiquitin-protein ligase RNF31
C: Ubiquitin-conjugating enzyme E2 D2
E: Polyubiquitin-B
G: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,13712
Polymers77,6144
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: E3 ubiquitin-protein ligase RNF31
B: E3 ubiquitin-protein ligase RNF31
C: Ubiquitin-conjugating enzyme E2 D2
D: Ubiquitin-conjugating enzyme E2 D2
E: Polyubiquitin-B
F: Polyubiquitin-B
G: Polyubiquitin-B
H: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,27424
Polymers155,2278
Non-polymers1,04716
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: E3 ubiquitin-protein ligase RNF31
D: Ubiquitin-conjugating enzyme E2 D2
F: Polyubiquitin-B
H: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,13712
Polymers77,6144
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
I: Ubiquitin-conjugating enzyme E2 D2


Theoretical massNumber of molelcules
Total (without water)16,9311
Polymers16,9311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.820, 75.740, 120.960
Angle α, β, γ (deg.)90.00, 95.56, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13C
23I
14D
24I
15E
25F
16E
26G
17E
27H
18F
28G
19F
29H
110G
210H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSILEILEAA699 - 10107 - 318
21CYSCYSILEILEBB699 - 10107 - 318
12LEULEUALAALACC3 - 1465 - 148
22LEULEUALAALADD3 - 1465 - 148
13LEULEUTYRTYRCC3 - 1455 - 147
23LEULEUTYRTYRII3 - 1455 - 147
14PROPROTYRTYRDD0 - 1452 - 147
24PROPROTYRTYRII0 - 1452 - 147
15METMETGLYGLYEE1 - 761 - 76
25METMETGLYGLYFF1 - 761 - 76
16METMETGLYGLYEE1 - 761 - 76
26METMETGLYGLYGG1 - 761 - 76
17METMETGLYGLYEE1 - 761 - 76
27METMETGLYGLYHH1 - 761 - 76
18METMETGLYGLYFF1 - 761 - 76
28METMETGLYGLYGG1 - 761 - 76
19METMETGLYGLYFF1 - 761 - 76
29METMETGLYGLYHH1 - 761 - 76
110METMETGLYGLYGG1 - 761 - 76
210METMETGLYGLYHH1 - 761 - 76

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein E3 ubiquitin-protein ligase RNF31 / HOIL-1-interacting protein / HOIP / RING finger protein 31 / Zinc in-between-RING-finger ubiquitin- ...HOIL-1-interacting protein / HOIP / RING finger protein 31 / Zinc in-between-RING-finger ubiquitin-associated domain protein


Mass: 43528.672 Da / Num. of mol.: 2 / Fragment: UNP residues 696-1072
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF31, ZIBRA / Production host: Escherichia coli (E. coli)
References: UniProt: Q96EP0, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein Ubiquitin-conjugating enzyme E2 D2 / (E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2 / p53-regulated ubiquitin-conjugating enzyme 1


Mass: 16931.404 Da / Num. of mol.: 3 / Mutation: S22R, C85K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Production host: Escherichia coli (E. coli)
References: UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#3: Protein
Polyubiquitin-B


Mass: 8576.831 Da / Num. of mol.: 4 / Fragment: UNP residues 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
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: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2- Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.282 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 3.48→29.69 Å / Num. obs: 22930 / % possible obs: 98.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 9.9
Reflection shellResolution: 3.48→3.72 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.875 / Mean I/σ(I) obs: 1.6 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
Aimlessdata scaling
XSCALEdata scaling
PHASERphasing
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LJP chains A and B; 3A33 chain A and 2CT7

4ljp

3a33

2ct7


Resolution: 3.48→29.69 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.895 / SU B: 110.566 / SU ML: 0.758 / Cross valid method: THROUGHOUT / ESU R Free: 0.745 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3026 1213 5 %RANDOM
Rwork0.24869 ---
obs0.25137 22930 98.53 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 185.764 Å2
Baniso -1Baniso -2Baniso -3
1-2.64 Å20 Å2-2.01 Å2
2---2.15 Å20 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 3.48→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10953 0 16 0 10969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01911276
X-RAY DIFFRACTIONr_bond_other_d0.0040.0210686
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.96715218
X-RAY DIFFRACTIONr_angle_other_deg1.2573.00424601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.54651347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03323.941538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.37151978
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9821581
X-RAY DIFFRACTIONr_chiral_restr0.1040.21632
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112585
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022597
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A298120.11
12B298120.11
21C175280.06
22D175280.06
31C168740.09
32I168740.09
41D173840.08
42I173840.08
51E97200.05
52F97200.05
61E96600.05
62G96600.05
71E95740.08
72H95740.08
81F97260.05
82G97260.05
91F96440.08
92H96440.08
101G97840.06
102H97840.06
LS refinement shellResolution: 3.482→3.573 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 84 -
Rwork0.385 1504 -
obs--89.87 %
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)
16.21840.19863.12.58221.19637.3476-0.11650.48390.72520.1495-0.2071-0.0264-0.69720.52530.32360.4692-0.0070.11830.60410.1550.4992330.22513.327401.4906
21.31140.7524-1.11068.6872.6762.8563-0.3132-0.140.04851.2245-0.98492.89380.8531-1.13481.29820.6293-0.26790.77161.5141-0.65521.6282274.8939-15.8018380.1825
36.03321.23134.06144.33543.29438.311-0.21440.3629-0.0873-0.2707-0.33610.60760.0473-0.43730.55050.3763-0.01330.11820.8055-0.10420.32296.341-18.8122359.1754
42.5325-1.2927-2.64455.16161.20714.6122-0.03280.21790.18860.4285-0.44441.3671-0.1365-1.59620.47720.66570.06080.09051.2874-0.48050.8765302.725314.068417.089
56.95490.0696-3.15253.1705-2.40224.73570.15351.0838-1.7715-0.0855-0.18551.82630.4081-0.6120.0320.6802-0.117-0.06291.5661-0.82812.2511258.742-14.1703363.1222
610.6254-3.2811-1.36254.03140.30396.25710.4553-0.7197-0.56380.6919-0.55090.5876-0.2865-0.49690.09561.2146-0.32480.23650.7656-0.13630.3242320.046810.0333438.0521
711.659-0.5526-2.424312.76011.33517.21370.3691.05011.7098-1.1977-0.2432-0.5339-0.651-0.1264-0.12580.47750.17950.17180.83040.0730.7914294.3977-1.6112368.966
811.6207-2.54460.542913.7713.56328.3927-0.10520.687-0.35730.08880.075-0.16211.21780.56610.03020.7686-0.05850.08160.54640.0530.2726322.3714-2.9407403.4342
97.5936-0.79562.18294.41220.954810.64740.20670.93491.6773-0.31980.1004-0.4645-0.71051.0952-0.30710.5984-0.26960.15061.36970.42940.8682344.316620.5846392.4927
1011.2617-0.28193.51069.54482.04911.0042-0.20521.0899-0.4098-0.4410.3644-0.35030.59320.5833-0.15920.4614-0.11260.25431.0477-0.11180.37308.4169-26.3302349.528
117.5983-3.9227-2.916110.99653.87098.3841-0.13170.29240.3641-0.74920.4335-0.0667-0.26830.1435-0.30190.70560.20180.15911.28510.15680.6211333.567736.9072369.4893
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A699 - 855
2X-RAY DIFFRACTION2A856 - 1011
3X-RAY DIFFRACTION3B699 - 848
4X-RAY DIFFRACTION4B849 - 1066
5X-RAY DIFFRACTION5C3 - 147
6X-RAY DIFFRACTION6D0 - 147
7X-RAY DIFFRACTION7E1 - 76
8X-RAY DIFFRACTION8F1 - 76
9X-RAY DIFFRACTION9G1 - 76
10X-RAY DIFFRACTION10H1 - 76
11X-RAY DIFFRACTION11I0 - 146

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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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