[English] 日本語
Yorodumi
- PDB-5f5u: Crystal structure of the Snu23-Prp38-MFAP1(217-258) complex of Ch... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f5u
TitleCrystal structure of the Snu23-Prp38-MFAP1(217-258) complex of Chaetomium thermophilum
Components
  • Prp38
  • Putative uncharacterized protein
  • Zinc finger domain-containing protein
KeywordsSPLICING / B-specific protein / heterotrimer / pre-mRNA splicing / SAH
Function / homology
Function and homology information


U4/U6 x U5 tri-snRNP complex / spliceosomal complex / mRNA splicing, via spliceosome / nucleic acid binding / zinc ion binding
Similarity search - Function
Micro-fibrillar-associated protein 1, C-terminal / Microfibrillar-associated protein 1 / Microfibril-associated/Pre-mRNA processing / U4/U6.U5 small nuclear ribonucleoprotein component Snu23 / Pre-mRNA-splicing factor 38 / PRP38 family / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger ...Micro-fibrillar-associated protein 1, C-terminal / Microfibrillar-associated protein 1 / Microfibril-associated/Pre-mRNA processing / U4/U6.U5 small nuclear ribonucleoprotein component Snu23 / Pre-mRNA-splicing factor 38 / PRP38 family / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Pre-mRNA-splicing factor 38 / Zinc finger domain-containing protein / Micro-fibrillar-associated protein 1 C-terminal domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.748 Å
AuthorsUlrich, A.K.C. / Seeger, M. / Bartlick, N. / Wahl, M.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationWA1126/7-1 Germany
CitationJournal: Structure / Year: 2016
Title: Scaffolding in the Spliceosome via Single alpha Helices.
Authors: Ulrich, A.K.C. / Seeger, M. / Schutze, T. / Bartlick, N. / Wahl, M.C.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Prp38
B: Putative uncharacterized protein
C: Zinc finger domain-containing protein
D: Prp38
E: Putative uncharacterized protein
F: Zinc finger domain-containing protein
G: Prp38
H: Putative uncharacterized protein
I: Zinc finger domain-containing protein


Theoretical massNumber of molelcules
Total (without water)119,8399
Polymers119,8399
Non-polymers00
Water1,820101
1
A: Prp38
B: Putative uncharacterized protein
C: Zinc finger domain-containing protein


Theoretical massNumber of molelcules
Total (without water)39,9463
Polymers39,9463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-15 kcal/mol
Surface area15150 Å2
MethodPISA
2
D: Prp38
E: Putative uncharacterized protein
F: Zinc finger domain-containing protein


Theoretical massNumber of molelcules
Total (without water)39,9463
Polymers39,9463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-17 kcal/mol
Surface area16180 Å2
MethodPISA
3
G: Prp38
H: Putative uncharacterized protein
I: Zinc finger domain-containing protein


Theoretical massNumber of molelcules
Total (without water)39,9463
Polymers39,9463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-15 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.960, 95.260, 133.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D
31chain G
12chain B
22chain E
32chain H
13chain C
23chain F
33chain I

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLUGLUchain AAA22 - 20925 - 212
21LEULEUASNASNchain DDD15 - 21618 - 219
31GLYGLYLYSLYSchain GGG22 - 21525 - 218
12GLYGLYARGARGchain BBB213 - 2571 - 45
22VALVALARGARGchain EEE221 - 2589 - 46
32THRTHRARGARGchain HHH217 - 2585 - 46
13GLYGLYSERSERchain CCC131 - 1623 - 34
23GLUGLUVALVALchain FFF132 - 1604 - 32
33VALVALVALVALchain III133 - 1605 - 32

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Prp38


Mass: 25617.205 Da / Num. of mol.: 3 / Fragment: NTR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0013190 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: G0S1D3
#2: Protein Putative uncharacterized protein


Mass: 10139.329 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0069660 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: G0SHD7
#3: Protein/peptide Zinc finger domain-containing protein


Mass: 4189.787 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0035280 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: G0S6R0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 4.75 / Details: 0.1M citric acid, pH 4.75, and 15% (w/v) PEG 6,000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.748→19.93 Å / Num. obs: 30180 / % possible obs: 99.5 % / Redundancy: 5 % / Rsym value: 0.15 / Net I/σ(I): 11.1
Reflection shellResolution: 2.748→2.82 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1 / % possible all: 98.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4rz9

4rz9


Resolution: 2.748→19.927 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2749 1524 5.06 %Random selection
Rwork0.2294 28618 --
obs0.2317 30142 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 263.64 Å2 / Biso mean: 92.5637 Å2 / Biso min: 32.87 Å2
Refinement stepCycle: final / Resolution: 2.748→19.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6577 0 0 101 6678
Biso mean---64.1 -
Num. residues----798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046688
X-RAY DIFFRACTIONf_angle_d0.8368993
X-RAY DIFFRACTIONf_chiral_restr0.033974
X-RAY DIFFRACTIONf_plane_restr0.0041172
X-RAY DIFFRACTIONf_dihedral_angle_d14.362630
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2809X-RAY DIFFRACTION9.967TORSIONAL
12D2809X-RAY DIFFRACTION9.967TORSIONAL
13G2809X-RAY DIFFRACTION9.967TORSIONAL
21B612X-RAY DIFFRACTION9.967TORSIONAL
22E612X-RAY DIFFRACTION9.967TORSIONAL
23H612X-RAY DIFFRACTION9.967TORSIONAL
31C423X-RAY DIFFRACTION9.967TORSIONAL
32F423X-RAY DIFFRACTION9.967TORSIONAL
33I423X-RAY DIFFRACTION9.967TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7483-2.83670.4331520.38232528268099
2.8367-2.93780.42611250.356825582683100
2.9378-3.0550.33481260.334225972723100
3.055-3.19350.35691390.315725692708100
3.1935-3.36120.32271320.27525732705100
3.3612-3.57060.3241370.24425822719100
3.5706-3.84450.27721530.220225842737100
3.8445-4.2280.20511400.191226052745100
4.228-4.83220.22161240.179226322756100
4.8322-6.05960.26051420.208526522794100
6.0596-19.92780.24631540.19842738289299
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)
16.2235-6.1969-5.29486.14895.17245.8868-1.4736-1.55-2.22991.28240.50122.28651.4068-0.21541.0770.83-0.13650.00751.51090.23221.370327.404528.7551160.7698
22.0862-1.9929-3.70732.14233.73359.5504-0.4795-0.3748-1.96680.56830.63740.34861.6737-0.1802-0.48580.77850.0623-0.06570.74940.19761.2641.463124.0121154.4802
30.23670.98850.49894.8488-0.25588.60170.8167-0.9343-1.24870.9682-0.0692-0.43150.08291.1052-0.51690.35030.1077-0.47481.2630.59370.7650.604233.1222161.4001
45.91710.0893-0.55926.0693-1.12384.38290.1746-0.5581-0.51250.31720.10190.15540.19270.0196-0.26270.34690.0319-0.03030.52640.16560.458740.694640.2768155.5003
53.4314-0.79193.63012.0837-1.2079.25360.2983-0.36620.83-0.2489-0.4736-0.30550.4872-0.04980.22670.37980.00580.02650.6910.04760.609925.275543.172150.0569
69.68-1.07982.35018.1141-4.9273.3690.31062.5017-0.9146-1.6108-0.3171-0.51420.57860.08810.13660.59770.1180.01871.0809-0.0360.737443.046842.9993141.2201
78.98362.7482-0.3731.6507-0.18243.98620.0291.025-0.5444-0.39430.14180.21750.6054-0.5745-0.11790.46310.0345-0.11840.62250.02730.706928.51237.2376143.6194
80.5516-1.1447-0.04376.61321.51250.45640.25041.60342.3528-0.57251.39052.0617-0.8642-1.5775-1.53140.69430.0955-0.28041.22090.45731.279318.679650.7681139.1758
96.60535.3074-1.4297.13452.5465.12071.5915-1.25360.66640.6730.7290.8078-0.03691.6081-1.83660.6149-0.0636-0.03050.994-0.05350.909246.349154.1868143.0144
103.94065.53422.21098.26054.38092.3498-0.1191.5138-0.2862-0.364-0.11020.45530.149-0.28920.28740.62650.0328-0.21051.26440.08251.058123.087843.9054130.3005
116.7861.01686.36243.50971.4166.1126-0.9346-0.4372-2.80533.26710.3427-0.71360.1120.11390.41480.8688-0.0390.06721.52540.41431.082940.765638.0163173.6375
124.5223-0.9824.25723.1866-0.76954.05960.0711-0.98270.89550.4346-0.4207-1.0935-0.94511.51140.54240.6617-0.06950.08841.03990.01430.992748.746555.7628160.9174
139.45652.8073-4.48134.258-3.37596.1396-1.0967-1.0216-0.7782-0.2760.3101-1.27531.07270.47460.66040.53990.01070.02520.90540.02991.076236.0585-8.7223130.8748
147.3353-0.2850.76973.7884-1.03694.68990.0552-0.39280.630.20620.0507-0.3519-0.15910.3495-0.10310.3568-0.02720.07270.576-0.09020.655339.46768.0519128.5094
156.22522.71722.70053.6588-0.7782.52280.03220.57350.6176-0.2857-0.0016-0.2062-0.1155-0.0676-0.07750.4695-0.01080.06740.72890.01280.675330.08729.092116.5035
161.3799-2.5934-1.54644.94432.91591.76260.5371.7537-0.2597-1.33110.54341.0465-0.39-0.7543-0.65881.84630.6220.05332.83530.64321.917124.819526.5473103.2837
173.2434.96462.21677.95393.51945.0061-0.20541.40920.1219-0.61650.0028-0.6343-0.3236-0.00730.35330.72710.09220.08820.9960.28140.990723.08613.3947104.7197
181.5939-1.21220.2960.9294-0.09938.0315-0.7557-0.8757-1.44120.74151.7941-1.64861.1628-0.1197-1.25340.80950.03-0.07771.3415-0.0631.306240.16835.0989145.0514
191.6848-0.26880.86726.0625-1.90935.3310.3929-1.03361.90430.0536-0.0465-0.6409-1.99281.1228-0.26741.053-0.32020.14981.1943-0.35481.381947.080122.76135.5338
202.59651.61671.36771.4448-0.56387.30060.1872-1.47330.81770.68540.37350.4742-0.5214-1.6487-0.58780.9780.48680.22371.9588-0.07331.01957.8611-6.6664155.3376
215.9914-4.8291-1.51317.11393.27751.7332-1.1546-2.2935-1.11312.480.86851.0098-1.3042-0.1570.42681.17170.5176-0.00421.92240.01590.62722.8083-9.2755158.6931
226.45872.5403-3.67626.28750.52112.8099-0.1567-1.65720.35081.2678-0.32770.96691.6728-1.23740.31641.04980.20590.30652.46020.25671.061410.7614-20.5322156.9289
231.7614-0.1730.26591.5861-0.84640.56690.0575-1.5060.48270.9601-0.39820.1649-1.0085-0.7237-0.60730.94070.78040.3562.3945-0.07380.46313.717-6.8032153.0577
245.74025.8283-0.98358.97583.41266.7212-1.2105-2.7271.87440.36061.4361-1.9339-0.26590.0139-0.3410.95660.5026-0.17511.0886-0.24460.71827.047-6.6557146.0349
253.6755-0.0737-2.12881.97962.1225.9234-0.48-1.7503-0.54570.31090.59130.5594-0.2985-0.9422-0.2460.410.11450.03731.08020.17050.563818.7023-15.6079142.9229
264.0487-1.5680.64086.1279-1.56070.36580.2575-0.8267-0.7427-0.80910.40940.57570.5007-0.8215-0.47690.50870.0905-0.08621.2610.27120.824914.6899-16.2701133.6602
270.9865-1.36640.42921.9438-0.78890.598-0.6498-0.51161.1153-1.1624-0.3597-0.2129-0.0621-0.84150.56881.43890.2157-0.24651.6226-0.29241.203928.3358-34.585122.0406
285.5524-4.7191-7.32776.09855.47569.96932.0346-1.59940.90240.61911.5252-1.4926-0.8593-2.4088-2.57230.7508-0.0607-0.06332.05530.62181.69631.1635-29.1939148.1419
297.864-4.1215.28566.6619-5.29346.46090.3021-0.1299-1.0474-1.13380.13750.89210.3935-0.6524-0.30650.81130.1793-0.24170.9071-0.1640.774315.2454-24.6218125.0501
307.9485-0.9035-3.23993.14252.86293.4596-0.3065-1.6169-0.80850.48630.3449-0.1253-0.15510.2729-0.21471.29380.3575-0.26951.914-0.38970.594333.9211-10.1031157.7065
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 30 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 45 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 57 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 127 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 128 through 142 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 143 through 155 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 190 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 191 through 206 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 213 through 222 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 223 through 257 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid 131 through 137 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 138 through 162 )C0
13X-RAY DIFFRACTION13chain 'D' and (resid 16 through 45 )D0
14X-RAY DIFFRACTION14chain 'D' and (resid 46 through 142 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 143 through 199 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 200 through 216 )D0
17X-RAY DIFFRACTION17chain 'E' and (resid 221 through 258 )E0
18X-RAY DIFFRACTION18chain 'F' and (resid 132 through 137 )F0
19X-RAY DIFFRACTION19chain 'F' and (resid 138 through 159 )F0
20X-RAY DIFFRACTION20chain 'G' and (resid 22 through 57 )G0
21X-RAY DIFFRACTION21chain 'G' and (resid 58 through 68 )G0
22X-RAY DIFFRACTION22chain 'G' and (resid 69 through 83 )G0
23X-RAY DIFFRACTION23chain 'G' and (resid 84 through 98 )G0
24X-RAY DIFFRACTION24chain 'G' and (resid 99 through 112 )G0
25X-RAY DIFFRACTION25chain 'G' and (resid 113 through 155 )G0
26X-RAY DIFFRACTION26chain 'G' and (resid 156 through 202 )G0
27X-RAY DIFFRACTION27chain 'G' and (resid 203 through 215 )G0
28X-RAY DIFFRACTION28chain 'H' and (resid 217 through 222 )H0
29X-RAY DIFFRACTION29chain 'H' and (resid 223 through 258 )H0
30X-RAY DIFFRACTION30chain 'I' and (resid 135 through 160 )I0

+
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://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