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- PDB-6cu0: Crystal structure of 4-1BBL/4-1BB (C121S) complex in P21 space group -

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Basic information

Entry
Database: PDB / ID: 6cu0
TitleCrystal structure of 4-1BBL/4-1BB (C121S) complex in P21 space group
Components
  • Tumor necrosis factor ligand superfamily member 9
  • Tumor necrosis factor receptor superfamily member 9
KeywordsCYTOKINE / complex
Function / homology
Function and homology information


tumor necrosis factor receptor superfamily binding / positive regulation of cytotoxic T cell differentiation / TNFs bind their physiological receptors / regulation of immature T cell proliferation in thymus / tumor necrosis factor receptor binding / positive regulation of activated T cell proliferation / regulation of T cell proliferation / cytokine activity / cell-cell signaling / signaling receptor activity ...tumor necrosis factor receptor superfamily binding / positive regulation of cytotoxic T cell differentiation / TNFs bind their physiological receptors / regulation of immature T cell proliferation in thymus / tumor necrosis factor receptor binding / positive regulation of activated T cell proliferation / regulation of T cell proliferation / cytokine activity / cell-cell signaling / signaling receptor activity / regulation of cell population proliferation / regulation of apoptotic process / immune response / signaling receptor binding / negative regulation of cell population proliferation / external side of plasma membrane / apoptotic process / extracellular space / plasma membrane
Similarity search - Function
Tumor necrosis factor ligand superfamily member 9 / Tumour necrosis factor receptor 9 / Tumour necrosis factor receptor 9, N-terminal / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region ...Tumor necrosis factor ligand superfamily member 9 / Tumour necrosis factor receptor 9 / Tumour necrosis factor receptor 9, N-terminal / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNF(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / Jelly Rolls - #40 / TNFR/NGFR cysteine-rich region / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily / Growth factor receptor cysteine-rich domain superfamily / Ribbon / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 9 / Tumor necrosis factor receptor superfamily member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsAruna, B. / Zajonc, D.M. / Doukov, T.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Crystal structures of the human 4-1BB receptor bound to its ligand 4-1BBL reveal covalent receptor dimerization as a potential signaling amplifier.
Authors: Bitra, A. / Doukov, T. / Croft, M. / Zajonc, D.M.
History
DepositionMar 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 4, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.5Nov 13, 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: Tumor necrosis factor ligand superfamily member 9
B: Tumor necrosis factor ligand superfamily member 9
C: Tumor necrosis factor ligand superfamily member 9
D: Tumor necrosis factor ligand superfamily member 9
E: Tumor necrosis factor ligand superfamily member 9
F: Tumor necrosis factor ligand superfamily member 9
G: Tumor necrosis factor receptor superfamily member 9
H: Tumor necrosis factor receptor superfamily member 9
J: Tumor necrosis factor receptor superfamily member 9
K: Tumor necrosis factor receptor superfamily member 9
L: Tumor necrosis factor receptor superfamily member 9
I: Tumor necrosis factor receptor superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,63114
Polymers194,18812
Non-polymers4422
Water79344
1
A: Tumor necrosis factor ligand superfamily member 9
B: Tumor necrosis factor ligand superfamily member 9
D: Tumor necrosis factor ligand superfamily member 9
G: Tumor necrosis factor receptor superfamily member 9
K: Tumor necrosis factor receptor superfamily member 9
I: Tumor necrosis factor receptor superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3157
Polymers97,0946
Non-polymers2211
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-52 kcal/mol
Surface area38050 Å2
MethodPISA
2
C: Tumor necrosis factor ligand superfamily member 9
E: Tumor necrosis factor ligand superfamily member 9
F: Tumor necrosis factor ligand superfamily member 9
H: Tumor necrosis factor receptor superfamily member 9
J: Tumor necrosis factor receptor superfamily member 9
L: Tumor necrosis factor receptor superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3157
Polymers97,0946
Non-polymers2211
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-48 kcal/mol
Surface area38640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.961, 114.745, 126.039
Angle α, β, γ (deg.)90.000, 101.240, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F
116G
216H
117G
217J
118G
218K
119G
219L
120G
220I
121H
221J
122H
222K
123H
223L
124H
224I
125J
225K
126J
226L
127J
227I
128K
228L
129K
229I
130L
230I

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
11METMETPROPROAA91 - 24212 - 163
21METMETPROPROBB91 - 24212 - 163
12METMETPROPROAA91 - 24212 - 163
22METMETPROPROCC91 - 24212 - 163
13METMETTHRTHRAA91 - 24112 - 162
23METMETTHRTHRDD91 - 24112 - 162
14METMETPROPROAA91 - 24212 - 163
24METMETPROPROEE91 - 24212 - 163
15METMETPROPROAA91 - 24212 - 163
25METMETPROPROFF91 - 24212 - 163
16METMETPROPROBB91 - 24212 - 163
26METMETPROPROCC91 - 24212 - 163
17METMETVALVALBB91 - 24012 - 161
27METMETVALVALDD91 - 24012 - 161
18METMETPROPROBB91 - 24212 - 163
28METMETPROPROEE91 - 24212 - 163
19METMETPROPROBB91 - 24212 - 163
29METMETPROPROFF91 - 24212 - 163
110GLYGLYTHRTHRCC90 - 24111 - 162
210GLYGLYTHRTHRDD90 - 24111 - 162
111METMETPROPROCC91 - 24212 - 163
211METMETPROPROEE91 - 24212 - 163
112GLYGLYPROPROCC90 - 24211 - 163
212GLYGLYPROPROFF90 - 24211 - 163
113METMETTHRTHRDD91 - 24112 - 162
213METMETTHRTHREE91 - 24112 - 162
114GLYGLYTHRTHRDD90 - 24111 - 162
214GLYGLYTHRTHRFF90 - 24111 - 162
115METMETPROPROEE91 - 24212 - 163
215METMETPROPROFF91 - 24212 - 163
116ASPASPCYSCYSGG26 - 1584 - 136
216ASPASPCYSCYSHH26 - 1584 - 136
117PROPROCYSCYSGG27 - 1585 - 136
217PROPROCYSCYSJI27 - 1585 - 136
118ASPASPVALVALGG26 - 1574 - 135
218ASPASPCYSCYSKJ26 - 1584 - 136
119SERSERCYSCYSGG29 - 1587 - 136
219SERSERCYSCYSLK29 - 1587 - 136
120ASPASPCYSCYSGG26 - 1584 - 136
220ASPASPCYSCYSIL26 - 1584 - 136
121PROPROCYSCYSHH27 - 1585 - 136
221PROPROCYSCYSJI27 - 1585 - 136
122ASPASPVALVALHH26 - 1564 - 134
222ASPASPVALVALKJ26 - 1574 - 135
123SERSERVALVALHH29 - 1577 - 135
223SERSERVALVALLK29 - 1577 - 135
124ASPASPCYSCYSHH26 - 1584 - 136
224ASPASPCYSCYSIL26 - 1584 - 136
125PROPROVALVALJI27 - 1575 - 135
225PROPROCYSCYSKJ27 - 1585 - 136
126SERSERCYSCYSJI29 - 1587 - 136
226SERSERCYSCYSLK29 - 1587 - 136
127PROPROCYSCYSJI27 - 1585 - 136
227PROPROCYSCYSIL27 - 1585 - 136
128SERSERVALVALKJ29 - 1577 - 135
228SERSERVALVALLK29 - 1567 - 134
129ASPASPCYSCYSKJ26 - 1584 - 136
229ASPASPVALVALIL26 - 1574 - 135
130SERSERCYSCYSLK29 - 1587 - 136
230SERSERCYSCYSIL29 - 1587 - 136

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30

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Components

#1: Protein
Tumor necrosis factor ligand superfamily member 9 / 4-1BB ligand / 4-1BBL


Mass: 17488.945 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF9
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: P41273
#2: Protein
Tumor necrosis factor receptor superfamily member 9 / 4-1BB ligand receptor / CDw137 / T-cell antigen 4-1BB homolog / T-cell antigen ILA


Mass: 14875.773 Da / Num. of mol.: 6 / Fragment: residues 23-160 / Mutation: C121S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF9, CD137, ILA
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q07011
#3: 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.: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M bicine and 30% W/V PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 32003 / % possible obs: 94.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.045 / Rrim(I) all: 0.097 / Χ2: 2.857 / Net I/σ(I): 17.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.313.50.54130270.8490.3110.6280.7889.5
3.31-3.454.20.40831660.9370.2170.4650.97795.4
3.45-3.64.40.26733190.9730.1410.3030.98498.9
3.6-3.794.40.16732990.9850.0880.191.34998
3.79-4.034.20.12432890.9920.0660.1422.0798.1
4.03-4.344.30.08132140.9960.0420.0923.35895.3
4.34-4.784.50.06833080.9960.0360.0773.64398.5
4.78-5.474.20.06632690.9950.0350.0764.44296.5
5.47-6.894.50.0733500.9940.0350.0795.01698.8
6.89-504.10.0827620.9880.0420.0915.82180

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X29, 5WI8

2x29

5wi8


Resolution: 3.2→50 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.884 / SU B: 75.43 / SU ML: 0.542 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.605
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1668 5.2 %RANDOM
Rwork0.2472 ---
obs0.2497 30300 94.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 363.51 Å2 / Biso mean: 146.215 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-7.43 Å20 Å23.89 Å2
2--1 Å20 Å2
3----9.24 Å2
Refinement stepCycle: final / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11404 0 28 44 11476
Biso mean--196.52 204.08 -
Num. residues----1672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01911704
X-RAY DIFFRACTIONr_bond_other_d0.0020.029742
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.94616012
X-RAY DIFFRACTIONr_angle_other_deg0.928322461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.93751649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83124.801402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.634151420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9181537
X-RAY DIFFRACTIONr_chiral_restr0.0860.21861
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02113713
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022315
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A79480.04
12B79480.04
21A77360.04
22C77360.04
31A78060.04
32D78060.04
41A72860.04
42E72860.04
51A78420.05
52F78420.05
61B76580.03
62C76580.03
71B76400.03
72D76400.03
81B72660.05
82E72660.05
91B77120.05
92F77120.05
101C75680.05
102D75680.05
111C71220.05
112E71220.05
121C76100.04
122F76100.04
131D72300.05
132E72300.05
141D76420.05
142F76420.05
151E72320.05
152F72320.05
161G65260.04
162H65260.04
171G64720.04
172J64720.04
181G64140.04
182K64140.04
191G63260.05
192L63260.05
201G64200.04
202I64200.04
211H65000.04
212J65000.04
221H63880.04
222K63880.04
231H63260.06
232L63260.06
241H66260.02
242I66260.02
251J62480.03
252K62480.03
261J62440.06
262L62440.06
271J63400.04
272I63400.04
281K61420.06
282L61420.06
291K62940.04
292I62940.04
301L62460.06
302I62460.06
LS refinement shellResolution: 3.2→3.283 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 107 -
Rwork0.369 2080 -
all-2187 -
obs--88.08 %
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)
12.2547-0.9995-0.78943.2202-0.87621.92640.1730.3251-0.26140.7141-0.13180.133-0.4981-0.0417-0.04120.479-0.1066-0.02770.3809-0.00230.4123-15.267-74.604-3.005
21.7776-2.3451-0.20595.03452.15033.1462-0.16230.79850.30390.0668-0.17680.048-0.4710.47590.33910.3506-0.1148-0.04090.82470.31480.3315-20.526-65.967-24.186
31.72340.1281-0.1824.77842.21032.1179-0.40660.0903-0.1284-0.14740.3606-0.1579-0.1050.00580.04610.4085-0.09740.14710.4594-0.05110.386119.05-15.114-50.777
40.4787-1.3758-0.31845.6705-0.68583.1820.04770.1124-0.2490.05920.28330.7248-0.1567-0.2402-0.3310.02690.0673-0.01790.53410.0880.8211-34.737-80.628-13.215
51.5491-0.9359-0.64683.4621.21331.6282-0.2926-0.3604-0.39920.15050.09970.02340.00920.05010.19290.4310.10420.17240.5260.16950.4278.872-26.931-33.645
62.9025-0.6973-0.58894.0513-0.05282.8181-0.61490.3701-0.3241-0.04540.26190.21860.0171-0.33060.3530.4291-0.25410.04640.6291-0.13240.2856-2.697-22.988-52.953
71.0036-1.6313-1.26434.4461.94261.63780.4136-0.06590.0899-0.5413-0.3253-0.3868-0.58240.2178-0.08820.4791-0.0929-0.02870.4813-0.01110.53068.097-74.215-17.972
83.2004-2.1155-2.3172.7971.6581.8743-0.759-0.2789-0.53620.34880.14290.69070.48210.02890.61610.4065-0.02570.08440.48920.02820.6137-17.528-23.021-26.163
91.0901-1.1609-0.30436.12860.31871.00250.3030.73380.4475-1.34390.0511-0.0645-0.0434-0.7295-0.35410.5989-0.1844-0.00691.48610.43530.2965-2.7472.613-64.546
101.30780.49320.21911.05660.2331.2857-0.33510.312-0.733-1.1505-0.13550.7545-1.10780.6160.47062.05580.1189-1.30411.2532-0.23061.7738-32.063-81.378-43.948
110.9947-0.7057-0.9094.93852.8912.7808-0.2844-0.2106-0.28680.42150.55060.01120.1240.4658-0.26620.41490.1677-0.08550.5947-0.02960.620326.164-3.612-27.008
123.8938-4.3442-0.63037.8577-0.08980.4181-0.7845-0.2569-0.08661.94310.87950.36940.00230.0643-0.09510.83830.36150.04890.69090.07550.391-24.75-102.9090.016
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A91 - 242
2X-RAY DIFFRACTION2B91 - 242
3X-RAY DIFFRACTION3C90 - 242
4X-RAY DIFFRACTION4D90 - 241
5X-RAY DIFFRACTION5E91 - 242
6X-RAY DIFFRACTION6F90 - 242
7X-RAY DIFFRACTION7G26 - 159
8X-RAY DIFFRACTION8H26 - 159
9X-RAY DIFFRACTION9J27 - 158
10X-RAY DIFFRACTION10K25 - 158
11X-RAY DIFFRACTION11L26 - 158
12X-RAY DIFFRACTION12I26 - 158

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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

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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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