[English] 日本語
Yorodumi
- PDB-4x0q: Ternary complex of human DNA polymerase theta C-terminal domain b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4x0q
TitleTernary complex of human DNA polymerase theta C-terminal domain binding ddGTP opposite dCMP
Components
  • DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*G)-3')
  • DNA (5'-D(P*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')
  • DNA polymerase theta
KeywordsTransferase/DNA / DNA polymerase / Transferase-DNA complex
Function / homology
Function and homology information


double-strand break repair via alternative nonhomologous end joining / HDR through MMEJ (alt-NHEJ) / single-stranded DNA helicase activity / replication fork processing / mitochondrial nucleoid / site of DNA damage / 5'-deoxyribose-5-phosphate lyase activity / error-prone translesion synthesis / negative regulation of double-strand break repair via homologous recombination / somatic hypermutation of immunoglobulin genes ...double-strand break repair via alternative nonhomologous end joining / HDR through MMEJ (alt-NHEJ) / single-stranded DNA helicase activity / replication fork processing / mitochondrial nucleoid / site of DNA damage / 5'-deoxyribose-5-phosphate lyase activity / error-prone translesion synthesis / negative regulation of double-strand break repair via homologous recombination / somatic hypermutation of immunoglobulin genes / DNA helicase activity / base-excision repair / protein homooligomerization / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / double-strand break repair / site of double-strand break / DNA helicase / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA repair / DNA damage response / chromatin binding / magnesium ion binding / Golgi apparatus / ATP hydrolysis activity / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
: / : / DNA_pol_Q helicase like region helical domain / Domain of unknown function (DUF7898) / DNA polymerase theta-like, helix-turn-helix domain / Helix-turn-helix domain / Alpha-Beta Plaits - #370 / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site ...: / : / DNA_pol_Q helicase like region helical domain / Domain of unknown function (DUF7898) / DNA polymerase theta-like, helix-turn-helix domain / Helix-turn-helix domain / Alpha-Beta Plaits - #370 / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 5' to 3' exonuclease, C-terminal subdomain / Helicase conserved C-terminal domain / DNA polymerase; domain 1 / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase theta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsZahn, K.E. / Doublie, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA052040 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Human DNA polymerase theta grasps the primer terminus to mediate DNA repair.
Authors: Zahn, K.E. / Averill, A.M. / Aller, P. / Wood, R.D. / Doublie, S.
History
DepositionNov 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase theta
B: DNA polymerase theta
E: DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*G)-3')
F: DNA (5'-D(P*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')
G: DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*G)-3')
H: DNA (5'-D(P*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,18214
Polymers191,7836
Non-polymers1,3998
Water00
1
A: DNA polymerase theta
E: DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*G)-3')
F: DNA (5'-D(P*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5917
Polymers95,8913
Non-polymers7004
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-27 kcal/mol
Surface area33740 Å2
MethodPISA
2
B: DNA polymerase theta
G: DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*G)-3')
H: DNA (5'-D(P*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5917
Polymers95,8913
Non-polymers7004
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-26 kcal/mol
Surface area33780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.704, 135.392, 159.819
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein DNA polymerase theta / DNA polymerase eta


Mass: 86735.461 Da / Num. of mol.: 2 / Fragment: UNP residues 1815-2590
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLQ, POLH / Plasmid: pSUMO3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: O75417, DNA-directed DNA polymerase

-
DNA chain , 2 types, 4 molecules EGFH

#2: DNA chain DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*G)-3')


Mass: 5157.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')


Mass: 3998.595 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 3 types, 8 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-DG3 / 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 2000mme, MPD, potassium chloride, TRIS buffer, glycerol
PH range: 8-8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.9→40 Å / Num. obs: 31372 / % possible obs: 85.6 % / Redundancy: 22.6 % / Net I/σ(I): 12.5

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
DENZOdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XOP

4xop


Resolution: 3.9→29.927 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 40.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3163 1581 5.04 %Random selection
Rwork0.2575 ---
obs0.2605 31372 82.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.9→29.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9926 890 86 0 10902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01411202
X-RAY DIFFRACTIONf_angle_d1.16915284
X-RAY DIFFRACTIONf_dihedral_angle_d18.5154250
X-RAY DIFFRACTIONf_chiral_restr0.0461706
X-RAY DIFFRACTIONf_plane_restr0.0051794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-4.02560.45351070.34991987X-RAY DIFFRACTION60
4.0256-4.16910.37151160.3352109X-RAY DIFFRACTION65
4.1691-4.33560.37151160.28692226X-RAY DIFFRACTION67
4.3356-4.53220.34541270.2912386X-RAY DIFFRACTION72
4.5322-4.77030.33741260.26822466X-RAY DIFFRACTION76
4.7703-5.06780.3861470.27012674X-RAY DIFFRACTION81
5.0678-5.45690.3341580.27692947X-RAY DIFFRACTION90
5.4569-6.00210.36121700.30533225X-RAY DIFFRACTION98
6.0021-6.86150.38391720.28033254X-RAY DIFFRACTION99
6.8615-8.61050.34011710.23513277X-RAY DIFFRACTION99
8.6105-29.92830.19591710.19063240X-RAY DIFFRACTION98
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)
10.53990.7131-0.9031.3621-1.81242.0652-0.09460.3922-0.6336-1.4068-0.037-0.12170.42060.32790.01281.78780.1578-0.07421.0867-0.66991.069121.0249147.42949.8917
20.3677-0.5881-0.36481.06980.01553.43360.00550.0888-0.02-0.0832-0.1950.14331.2828-0.24180.44871.15380.19390.44040.6246-0.92881.3259112.7352143.994225.5981
38.1172.8210.44292.91590.48882.8298-0.5874-2.3994-2.31461.29470.1973-1.4370.11171.29750.0891.18340.37520.03191.94560.17811.5914137.5036132.156652.8357
40.74490.1806-1.25251.92440.02232.2007-0.2338-0.0632-1.2053-0.6406-2.3176-0.7711.22161.80522.18692.530.44960.61851.89190.54613.1575135.9555113.335153.8259
53.910.8906-0.79462.6907-1.24992.26060.4321-0.6164-0.01460.0848-0.16180.0928-0.49610.5156-0.3060.6478-0.1039-0.02091.1013-0.52971.0451125.9817141.85243.1798
62.84571.295-1.33553.7203-0.70273.03450.7398-0.1225-0.17390.4378-0.38430.80990.4695-0.0682-0.34540.76520.08430.06540.7126-0.18051.7788106.0261120.411543.8894
73.23330.18581.02613.3865-0.61980.87480.69850.5927-1.2035-0.36920.3743-0.7793-0.35560.21190.81820.77550.59280.5411-0.0744-1.3151.4807108.2147133.990132.5505
83.7925-0.2873-0.76510.54570.56981.85560.83470.99550.0362-0.9705-0.6813-0.7868-0.9149-0.7897-0.12961.62890.3938-0.23730.848-0.29292.287120.9606161.737131.5176
91.6240.79121.28982.9021-0.55091.5020.2197-1.33690.26381.29830.3650.9725-0.53960.0419-0.43150.70750.03310.14210.9468-0.71731.9779109.2709146.634544.4681
100.67830.602-0.36452.29051.69462.45740.31470.40440.2713-1.525-0.6457-0.65820.4195-0.11390.28711.85250.15620.1541.1065-0.05010.4231117.32655.664110.0144
111.21830.6056-0.09850.93180.50263.42680.39180.2346-0.0138-0.9848-0.3499-0.3101-0.89830.3779-0.67540.73180.60340.34171.0931-0.42750.8919125.718159.042525.7985
120.1672-0.150.64141.1329-1.53583.17460.0217-0.87480.9770.7488-0.38421.1866-1.082-1.44120.40791.3035-0.22230.36631.7083-1.6491.8443100.646571.136452.5013
130.04080.0384-0.05980.8306-0.79860.7569-0.4033-1.27071.19431.2378-1.96441.1728-0.4339-1.51391.7661.7138-0.1317-0.51041.9517-1.00763.1079101.794189.85453.8116
142.76150.00730.90633.5241-1.2471.1618-0.8478-0.5626-0.00730.5502-0.61220.2288-0.1753-0.4148-0.09080.41190.14660.04711.1395-1.21261.0049112.165961.282343.2006
150.86160.0920.67973.74960.19232.1726-0.0213-0.32240.38110.786-0.65020.1871-0.17610.2120.37250.9582-0.06980.0651.0431-0.75092.3412132.102582.736344.1009
164.1140.6162-0.26052.74-0.11072.4960.3053-0.12091.72350.09090.5406-0.26630.43190.3282-0.37741.00390.10450.35740.7557-0.42621.121130.061469.069832.7952
173.9479-0.29410.5113.0786-0.13751.98020.82510.8846-0.7519-1.2097-0.5246-0.38211.70410.3989-0.25681.1434-0.1687-0.22210.8095-0.78071.9651117.376141.306831.6883
181.75460.5361-1.83832.3423-1.15622.28840.0618-1.2440.29290.8209-0.6315-0.63770.61530.05410.03591.19510.0448-0.70790.9693-0.47880.7535128.918256.536344.6419
190.12470.38170.1131.6604-1.21553.79430.6263-0.2352-1.193-0.0802-0.1923-1.19150.75361.4603-0.3591.09470.2095-0.23381.1395-0.55962.889126.2396119.759335.1935
200.66570.8446-0.92725.24754.17779.86180.75810.7068-0.3735-1.67571.2412-0.75761.49270.4119-2.06781.9601-0.2597-0.41261.2714-0.06541.5647127.7813122.804136.8922
210.49210.8559-1.26182.8499-1.65743.40180.80180.27072.18780.0518-0.131.2857-0.1739-0.8405-0.10060.92520.3216-0.17521.1916-0.82132.2272112.047583.371235.0476
222.83721.5644-2.15844.5155-2.2353.15280.3990.2227-0.4238-1.88540.7171.22970.04750.1357-0.37861.46340.0784-0.28580.7159-0.86471.9099110.39880.394236.7368
230.0881-0.22410.17942.32671.3092.1425-0.6007-0.986-0.0528-0.01140.11720.23261.0441-0.00080.61070.80380.35020.19690.7130.11952.235112.3228130.756246.1083
240.39240.0964-0.20111.01670.18140.75560.2297-0.1667-0.01470.2589-0.29550.0375-0.5903-0.0560.18750.96620.0384-0.73420.8876-0.74360.7984126.193372.578245.895
25-0.0258-0.00480.0446-0.0079-0.0021-0.06790.16160.24590.44280.30990.3604-0.020.23930.2956-0.20630.77840.12280.31970.8739-0.47040.792119.721101.832931.5301
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1824:2068 )A1824 - 2068
2X-RAY DIFFRACTION2( CHAIN A AND RESID 2069:2092 )A2069 - 2092
3X-RAY DIFFRACTION3( CHAIN A AND ( RESID 2093:2124 OR RESID 2192:2217 ) )A2093 - 2124
4X-RAY DIFFRACTION3( CHAIN A AND ( RESID 2093:2124 OR RESID 2192:2217 ) )A2192 - 2217
5X-RAY DIFFRACTION4( CHAIN A AND RESID 2125:2191 )A2125 - 2191
6X-RAY DIFFRACTION5( CHAIN A AND RESID 2218:2323 )A2218 - 2323
7X-RAY DIFFRACTION6( CHAIN A AND RESID 2332:2459 )A2332 - 2459
8X-RAY DIFFRACTION7( CHAIN A AND RESID 2460:2495 )A2460 - 2495
9X-RAY DIFFRACTION8( CHAIN A AND RESID 2496:2532 )A2496 - 2532
10X-RAY DIFFRACTION9( CHAIN A AND ( RESID 2324:2331 OR RESID 2533:2590 ) )A2324 - 2331
11X-RAY DIFFRACTION9( CHAIN A AND ( RESID 2324:2331 OR RESID 2533:2590 ) )A2533 - 2590
12X-RAY DIFFRACTION10( CHAIN B AND RESID 1824:2068 )B1824 - 2068
13X-RAY DIFFRACTION11( CHAIN B AND RESID 2069:2092 )B2069 - 2092
14X-RAY DIFFRACTION12( CHAIN B AND ( RESID 2093:2124 OR RESID 2192:2217 ) )B2093 - 2124
15X-RAY DIFFRACTION12( CHAIN B AND ( RESID 2093:2124 OR RESID 2192:2217 ) )B2192 - 2217
16X-RAY DIFFRACTION13( CHAIN B AND RESID 2125:2191 )B2125 - 2191
17X-RAY DIFFRACTION14( CHAIN B AND RESID 2218:2323 )B2218 - 2323
18X-RAY DIFFRACTION15( CHAIN B AND RESID 2332:2459 )B2332 - 2459
19X-RAY DIFFRACTION16( CHAIN B AND RESID 2460:2495 )B2460 - 2495
20X-RAY DIFFRACTION17( CHAIN B AND RESID 2496:2532 )B2496 - 2532
21X-RAY DIFFRACTION18( CHAIN B AND ( RESID 2324:2331 OR RESID 2533:2590 ) )B2324 - 2331
22X-RAY DIFFRACTION18( CHAIN B AND ( RESID 2324:2331 OR RESID 2533:2590 ) )B2533 - 2590
23X-RAY DIFFRACTION19( CHAIN E AND RESID 1:13 )E1 - 13
24X-RAY DIFFRACTION20( CHAIN F AND RESID 5:13 )F5 - 13
25X-RAY DIFFRACTION21( CHAIN G AND RESID 1:13 )G1 - 13
26X-RAY DIFFRACTION22( CHAIN H AND RESID 5:13 )H5 - 13
27X-RAY DIFFRACTION23( CHAIN A AND ( RESID 2604:2604 OR RESID 2603:2603 ) )A2604
28X-RAY DIFFRACTION23( CHAIN A AND ( RESID 2604:2604 OR RESID 2603:2603 ) )A2603
29X-RAY DIFFRACTION24( CHAIN B AND ( RESID 2604:2604 OR RESID 2603:2603 ) )B2604
30X-RAY DIFFRACTION24( CHAIN B AND ( RESID 2604:2604 OR RESID 2603:2603 ) )B2603
31X-RAY DIFFRACTION25( CHAIN A AND RESID 2601:2602 ) OR ( CHAIN B AND RESID 2601:2602 )A2601 - 2602
32X-RAY DIFFRACTION25( CHAIN A AND RESID 2601:2602 ) OR ( CHAIN B AND RESID 2601:2602 )B2601 - 2602

+
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