[English] 日本語
Yorodumi
- PDB-6tun: Helicase domain complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tun
TitleHelicase domain complex
Components
  • CDK-activating kinase assembly factor MAT1
  • General transcription and DNA repair factor IIH helicase subunit XPD
KeywordsNUCLEAR PROTEIN / Helicase / DNA-repair / Transcription / Cell Cylcle
Function / homology
Function and homology information


MMXD complex / Cytosolic iron-sulfur cluster assembly / central nervous system myelin formation / positive regulation of mitotic recombination / hair cell differentiation / hair follicle maturation / ventricular system development / CAK-ERCC2 complex / transcription factor TFIIK complex / UV protection ...MMXD complex / Cytosolic iron-sulfur cluster assembly / central nervous system myelin formation / positive regulation of mitotic recombination / hair cell differentiation / hair follicle maturation / ventricular system development / CAK-ERCC2 complex / transcription factor TFIIK complex / UV protection / embryonic cleavage / DNA 5'-3' helicase / adult heart development / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / transcription factor TFIID complex / spinal cord development / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / hematopoietic stem cell proliferation / erythrocyte maturation / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / bone mineralization / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / regulation of G1/S transition of mitotic cell cycle / intrinsic apoptotic signaling pathway by p53 class mediator / RNA Polymerase I Transcription Initiation / hematopoietic stem cell differentiation / embryonic organ development / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / transcription elongation by RNA polymerase I / Formation of HIV elongation complex in the absence of HIV Tat / transcription-coupled nucleotide-excision repair / Cyclin E associated events during G1/S transition / DNA helicase activity / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / RNA Polymerase II Transcription Elongation / cyclin-dependent protein kinase holoenzyme complex / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / extracellular matrix organization / insulin-like growth factor receptor signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / post-embryonic development / determination of adult lifespan / isomerase activity / nucleotide-excision repair / chromosome segregation / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase I Promoter Escape / positive regulation of smooth muscle cell proliferation / NoRC negatively regulates rRNA expression / multicellular organism growth / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / spindle / G1/S transition of mitotic cell cycle / Formation of Incision Complex in GG-NER / response to calcium ion / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Cyclin D associated events in G1 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / protein-macromolecule adaptor activity / response to oxidative stress / in utero embryonic development / transcription by RNA polymerase II / damaged DNA binding / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / response to hypoxia / DNA repair / apoptotic process / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / ATP hydrolysis activity / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus
Similarity search - Function
RAD3/XPD family / Helical and beta-bridge domain / Helical and beta-bridge domain / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / ATP-dependent helicase Rad3/Chl1-like / Helicase-like, DEXD box c2 type / DEAD2 ...RAD3/XPD family / Helical and beta-bridge domain / Helical and beta-bridge domain / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / ATP-dependent helicase Rad3/Chl1-like / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / HELICc2 / ATP-dependent helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
General transcription and DNA repair factor IIH helicase subunit XPD / CDK-activating kinase assembly factor MAT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.07 Å
AuthorsSauer, F. / Kisker, C.
CitationJournal: Nat Commun / Year: 2020
Title: In TFIIH the Arch domain of XPD is mechanistically essential for transcription and DNA repair.
Authors: Peissert, S. / Sauer, F. / Grabarczyk, D.B. / Braun, C. / Sander, G. / Poterszman, A. / Egly, J.M. / Kuper, J. / Kisker, C.
History
DepositionJan 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: General transcription and DNA repair factor IIH helicase subunit XPD
B: General transcription and DNA repair factor IIH helicase subunit XPD
D: CDK-activating kinase assembly factor MAT1
C: CDK-activating kinase assembly factor MAT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7626
Polymers63,6914
Non-polymers712
Water2,720151
1
A: General transcription and DNA repair factor IIH helicase subunit XPD
D: CDK-activating kinase assembly factor MAT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8813
Polymers31,8462
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: General transcription and DNA repair factor IIH helicase subunit XPD
C: CDK-activating kinase assembly factor MAT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8813
Polymers31,8462
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.940, 78.350, 92.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein General transcription and DNA repair factor IIH helicase subunit XPD / TFIIH subunit XPD / Basic transcription factor 2 80 kDa subunit / BTF2 p80 / CXPD / DNA excision ...TFIIH subunit XPD / Basic transcription factor 2 80 kDa subunit / BTF2 p80 / CXPD / DNA excision repair protein ERCC-2 / DNA repair protein complementing XP-D cells / TFIIH basal transcription factor complex 80 kDa subunit / TFIIH p80 / Xeroderma pigmentosum group D-complementing protein


Mass: 22539.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Arch domain / Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC2, XPD, XPDC / Production host: Escherichia coli (E. coli) / References: UniProt: P18074, DNA helicase
#2: Protein CDK-activating kinase assembly factor MAT1 / CDK7/cyclin-H assembly factor / Cyclin-G1-interacting protein / Menage a trois / RING finger ...CDK7/cyclin-H assembly factor / Cyclin-G1-interacting protein / Menage a trois / RING finger protein 66 / RING finger protein MAT1 / p35 / p36


Mass: 9305.615 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MNAT1, CAP35, MAT1, RNF66 / Production host: Escherichia coli (E. coli) / References: UniProt: P51948
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris pH 8.5 25% PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0064 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0064 Å / Relative weight: 1
ReflectionResolution: 2.07→46.71 Å / Num. obs: 33675 / % possible obs: 99.6 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rpim(I) all: 0.038 / Net I/σ(I): 11.6
Reflection shellResolution: 2.07→2.13 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 2591 / CC1/2: 0.759 / Rpim(I) all: 0.439

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: SAD / Resolution: 2.07→46.71 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.63
RfactorNum. reflection% reflection
Rfree0.2273 1286 3.83 %
Rwork0.192 --
obs0.1933 33596 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.07→46.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3863 0 2 151 4016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074047
X-RAY DIFFRACTIONf_angle_d0.8885479
X-RAY DIFFRACTIONf_dihedral_angle_d17.8122522
X-RAY DIFFRACTIONf_chiral_restr0.047624
X-RAY DIFFRACTIONf_plane_restr0.005718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.15290.30881420.29223508X-RAY DIFFRACTION99
2.1529-2.25090.30431360.25033544X-RAY DIFFRACTION99
2.2509-2.36950.26661460.23323555X-RAY DIFFRACTION100
2.3695-2.5180.27541420.21933542X-RAY DIFFRACTION99
2.518-2.71240.23861400.2053571X-RAY DIFFRACTION99
2.7124-2.98530.2631450.20813569X-RAY DIFFRACTION100
2.9853-3.41720.25691490.19283596X-RAY DIFFRACTION99
3.4172-4.30480.18061190.16773648X-RAY DIFFRACTION99
4.3048-46.710.19931670.17113777X-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)
14.39672.7012-3.21118.5406-2.83186.68590.32080.09220.1130.80740.2740.4102-0.9106-0.2278-0.57050.43340.13880.04080.39840.03750.4974-23.091-9.694633.9899
29.20440.8132-2.15372.43870.21352.8593-0.51580.29930.0925-0.23980.52130.8181-0.0063-0.73130.12090.503-0.00940.08090.43360.01310.6843-30.6231-28.721538.6664
34.9407-1.08691.40312.4003-3.50566.1820.38980.4216-1.0254-1.254-0.0520.36850.9727-0.4082-0.10490.6619-0.004-0.08250.3311-0.03730.5085-21.6116-30.547830.8528
48.72934.1858-4.31775.1372-2.69646.07050.2358-0.08520.56690.41810.19240.4971-0.3745-0.0314-0.43340.36080.01730.06150.2687-0.0180.328-13.5578-14.172535.1888
56.8558-2.0681-3.6653.18042.76043.4035-0.4082-0.5310.61270.24180.7438-0.73580.05310.949-0.3740.6885-0.1674-0.02190.484-0.0080.4297-2.7044-3.71324.3418
63.79351.5309-3.71726.099-1.85113.66150.1866-0.0469-0.24790.1471-0.0659-0.3708-0.42470.1114-0.07710.4450.02750.02740.3440.00730.3259-4.5424-17.502430.1173
76.55070.6149-3.51967.52220.52536.21280.09690.60820.0087-0.1191-0.08521.0184-0.2311-0.59760.07890.4263-0.0084-0.00670.30410.01570.4186-23.8317-21.113328.8631
84.9631-4.2076-4.42125.33164.64587.46410.2414-0.0754-0.3464-0.3805-0.0780.5009-0.62930.017-0.01380.3395-0.0063-0.02520.27980.00870.3916-15.5634-18.642919.5898
90.3496-1.2654-1.94556.41283.50697.1959-0.2868-0.2448-0.45941.0820.9637-0.18441.19060.7201-0.72910.6340.1341-0.17880.4646-0.02220.4857-10.2624-39.34214.3018
108.0106-0.7649-1.94433.36342.62763.23070.2751-1.3441-0.74390.1852-0.04231.296-1.1308-0.5116-0.12070.8466-0.0672-0.1360.69950.10370.5345-16.0484-29.97715.5792
116.7005-5.08574.27953.7246-2.91744.35250.2238-0.0927-0.1436-0.30720.0040.09180.51490.1651-0.45470.4701-0.0594-0.12480.33250.01080.4322-23.7228-29.1867-14.305
127.8888-0.43824.1965.50731.97293.5456-0.30050.11070.4181-0.2110.06560.3885-0.4586-0.17930.15520.4325-0.004-0.13170.34820.00490.5147-30.0174-10.4119-15.0789
131.6092-1.00270.58125.7787-0.85020.6827-0.5633-0.35840.9332-0.375-0.3370.3123-1.4129-0.19590.68350.63070.0388-0.08680.418-0.0690.4856-19.2241-8.6722-8.2439
146.3444-1.70842.70124.016-1.65256.20520.17720.6848-0.4745-0.72560.0512-0.1621-0.0630.4115-0.31620.4144-0.0291-0.03570.4-0.08280.4498-12.3436-25.5836-10.5717
154.78064.65812.79364.63793.21533.3967-0.29480.6929-0.8688-0.75050.1432-0.9301-0.19491.2233-0.51430.70490.1373-0.29230.5702-0.20970.8106-1.354-35.15640.724
165.2777-0.75373.17697.43-3.94234.0482-0.25870.3472-0.2117-0.36060.0805-0.9299-0.59850.8560.12950.3411-0.03110.05070.4896-0.14220.4331-3.9234-21.0396-5.5386
172.81731.45082.81494.62611.91647.4296-0.2439-0.7560.18540.08090.14890.5711-0.3244-0.23350.13010.4325-0.025-0.04230.29790.00810.4373-20.0126-16.6677-3.9545
187.8154-6.71225.7396.1075-5.83867.3287-0.5325-1.0164-0.55220.11150.88382.3911-0.1985-2.7585-0.60970.74050.0777-0.32360.7349-0.08410.8178-32.3568-27.3667-8.1223
199.14014.6344.72265.47215.88967.02230.2594-0.5811-0.15080.4418-0.1873-0.01270.3177-0.1837-0.07940.33780.0079-0.05170.3225-0.00160.3417-17.1462-24.30560.3738
205.31944.23434.46153.62844.00024.28110.32850.50270.2613-0.00770.08880.3715-0.49120.307-0.51810.48930.0239-0.02210.3483-0.0220.3171-7.3595-11.476814.4064
210.90081.74712.63663.42754.48276.8092-0.46150.27020.4535-1.09250.09241.4655-1.63850.37390.32060.8176-0.10090.03920.4676-0.01610.5811-10.80220.039419.8965
229.1852-3.35021.41953.1234-2.77313.4984-0.2505-0.82950.40620.97530.4592-0.3379-0.60190.3081-0.32290.5677-0.01750.01360.5178-0.0280.3116-6.7016-18.815944.7486
232.75692.7790.0455.41163.26527.4536-0.0671-0.2064-0.36360.16710.2797-0.41150.07950.2957-0.12690.46440.04910.02570.31450.0230.3542-10.9945-31.959739.6877
244.4519-0.0136-2.81097.44182.22282.6735-0.1781-1.6048-1.06791.3004-0.0239-0.40710.90990.99680.10431.02110.2619-0.00690.84780.17210.6574-7.9498-31.600552.8598
254.3557-0.53162.32723.34292.05383.29110.19831.1113-0.8449-0.5490.6048-0.90171.13670.8399-0.90510.84410.01890.07950.7315-0.07370.5688-5.7641-20.7904-20.4117
264.6315-1.80760.16739.3553.20577.0848-0.18360.28280.1045-0.85590.165-0.1369-0.5332-0.15880.00550.5798-0.1085-0.02840.39950.04470.3361-9.924-7.4111-15.615
271.4975-2.8546-0.50955.72821.28990.38320.63981.40130.5399-3.0631-1.1155-1.6367-1.5680.5110.95951.8867-0.27660.33141.1150.26810.8639-7.6331-8.3712-29.044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 246 through 276 )
2X-RAY DIFFRACTION2chain 'A' and (resid 277 through 289 )
3X-RAY DIFFRACTION3chain 'A' and (resid 290 through 325 )
4X-RAY DIFFRACTION4chain 'A' and (resid 326 through 343 )
5X-RAY DIFFRACTION5chain 'A' and (resid 344 through 353 )
6X-RAY DIFFRACTION6chain 'A' and (resid 354 through 368 )
7X-RAY DIFFRACTION7chain 'A' and (resid 369 through 391 )
8X-RAY DIFFRACTION8chain 'A' and (resid 392 through 419 )
9X-RAY DIFFRACTION9chain 'A' and (resid 420 through 439 )
10X-RAY DIFFRACTION10chain 'B' and (resid 246 through 252 )
11X-RAY DIFFRACTION11chain 'B' and (resid 253 through 276 )
12X-RAY DIFFRACTION12chain 'B' and (resid 277 through 289 )
13X-RAY DIFFRACTION13chain 'B' and (resid 290 through 325 )
14X-RAY DIFFRACTION14chain 'B' and (resid 326 through 344 )
15X-RAY DIFFRACTION15chain 'B' and (resid 345 through 353 )
16X-RAY DIFFRACTION16chain 'B' and (resid 354 through 368 )
17X-RAY DIFFRACTION17chain 'B' and (resid 369 through 385 )
18X-RAY DIFFRACTION18chain 'B' and (resid 386 through 394 )
19X-RAY DIFFRACTION19chain 'B' and (resid 395 through 409 )
20X-RAY DIFFRACTION20chain 'B' and (resid 410 through 419 )
21X-RAY DIFFRACTION21chain 'B' and (resid 420 through 439 )
22X-RAY DIFFRACTION22chain 'D' and (resid 66 through 81 )
23X-RAY DIFFRACTION23chain 'D' and (resid 82 through 111 )
24X-RAY DIFFRACTION24chain 'D' and (resid 112 through 130 )
25X-RAY DIFFRACTION25chain 'C' and (resid 65 through 81 )
26X-RAY DIFFRACTION26chain 'C' and (resid 82 through 111 )
27X-RAY DIFFRACTION27chain 'C' and (resid 112 through 129 )

+
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