[English] 日本語
Yorodumi
- PDB-4x0p: Ternary complex of human DNA polymerase theta C-terminal domain b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4x0p
TitleTernary complex of human DNA polymerase theta C-terminal domain binding ddATP opposite a tetrahydrofuran AP site analog
Components
  • DNA (5'-D(*CP*GP*TP*TP*GP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
  • DNA (5'-D(P*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*C)-3')
  • DNA polymerase theta
KeywordsTransferase/DNA / DNA Polymerase Alternative End-joining Translesion DNA Synthesis Cancer / 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'-dideoxyadenosine triphosphate / DNA / DNA (> 10) / DNA polymerase theta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.911 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 21, 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
C: DNA polymerase theta
D: DNA polymerase theta
F: DNA (5'-D(P*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*C)-3')
E: DNA (5'-D(*CP*GP*TP*TP*GP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
H: DNA (5'-D(P*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*C)-3')
G: DNA (5'-D(*CP*GP*TP*TP*GP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
J: DNA (5'-D(P*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*C)-3')
I: DNA (5'-D(*CP*GP*TP*TP*GP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
L: DNA (5'-D(P*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*C)-3')
K: DNA (5'-D(*CP*GP*TP*TP*GP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)399,14128
Polymers396,34312
Non-polymers2,79816
Water00
1
A: DNA polymerase theta
F: DNA (5'-D(P*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*C)-3')
E: DNA (5'-D(*CP*GP*TP*TP*GP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7857
Polymers99,0863
Non-polymers6994
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-19 kcal/mol
Surface area36040 Å2
MethodPISA
2
B: DNA polymerase theta
H: DNA (5'-D(P*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*C)-3')
G: DNA (5'-D(*CP*GP*TP*TP*GP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7857
Polymers99,0863
Non-polymers6994
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-20 kcal/mol
Surface area35510 Å2
MethodPISA
3
C: DNA polymerase theta
J: DNA (5'-D(P*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*C)-3')
I: DNA (5'-D(*CP*GP*TP*TP*GP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7857
Polymers99,0863
Non-polymers6994
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-26 kcal/mol
Surface area35760 Å2
MethodPISA
4
D: DNA polymerase theta
L: DNA (5'-D(P*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*C)-3')
K: DNA (5'-D(*CP*GP*TP*TP*GP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7857
Polymers99,0863
Non-polymers6994
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-21 kcal/mol
Surface area35770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.921, 136.971, 247.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
DNA polymerase theta / DNA polymerase eta


Mass: 89585.555 Da / Num. of mol.: 4 / Fragment: UNP residues 1792-2590
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, 8 molecules FHJLEGIK

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


Mass: 3958.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain
DNA (5'-D(*CP*GP*TP*TP*GP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')


Mass: 5541.592 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 3 types, 16 molecules

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


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-DDS / 2',3'-dideoxyadenosine triphosphate


Mass: 475.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O11P3

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 2000mme, MPD, potassium chloride, calcium 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: Feb 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.9→29.994 Å / Num. obs: 74685 / % possible obs: 99.7 % / Redundancy: 16.7 % / Rmerge(I) obs: 0.205 / Net I/σ(I): 16.7

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QSY

1qsy


Resolution: 3.911→29.994 Å / SU ML: 0.67 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 34.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3016 3805 5.09 %Random selection
Rwork0.2407 ---
obs0.2438 74685 99.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.911→29.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19852 2428 168 0 22448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01523127
X-RAY DIFFRACTIONf_angle_d1.36331686
X-RAY DIFFRACTIONf_dihedral_angle_d19.0368830
X-RAY DIFFRACTIONf_chiral_restr0.0573543
X-RAY DIFFRACTIONf_plane_restr0.0063617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.911-3.960.43891400.39422403X-RAY DIFFRACTION90
3.96-4.0120.39441450.35612578X-RAY DIFFRACTION99
4.012-4.06680.41331190.35242640X-RAY DIFFRACTION99
4.0668-4.12480.38471490.33652620X-RAY DIFFRACTION99
4.1248-4.18620.38791350.33612629X-RAY DIFFRACTION99
4.1862-4.25140.3011310.31932610X-RAY DIFFRACTION98
4.2514-4.32090.33411160.29982636X-RAY DIFFRACTION99
4.3209-4.39520.34171610.28822578X-RAY DIFFRACTION99
4.3952-4.47490.31211500.27982605X-RAY DIFFRACTION99
4.4749-4.56070.32181330.26922686X-RAY DIFFRACTION99
4.5607-4.65340.28941440.26952622X-RAY DIFFRACTION100
4.6534-4.75420.30451370.25392596X-RAY DIFFRACTION100
4.7542-4.86440.30191400.24292682X-RAY DIFFRACTION100
4.8644-4.98550.35411380.26422626X-RAY DIFFRACTION100
4.9855-5.11960.26661550.25592624X-RAY DIFFRACTION100
5.1196-5.26950.30981440.25642697X-RAY DIFFRACTION100
5.2695-5.43860.33161390.25692617X-RAY DIFFRACTION100
5.4386-5.63180.3861230.27112656X-RAY DIFFRACTION100
5.6318-5.85570.34731540.27162633X-RAY DIFFRACTION100
5.8557-6.120.35341450.28312638X-RAY DIFFRACTION100
6.12-6.43970.39681360.27592674X-RAY DIFFRACTION100
6.4397-6.83870.32981360.26012641X-RAY DIFFRACTION100
6.8387-7.35950.35051520.24752640X-RAY DIFFRACTION100
7.3595-8.08690.28921450.20142644X-RAY DIFFRACTION100
8.0869-9.22710.22941450.18682648X-RAY DIFFRACTION100
9.2271-11.51480.23371480.15512653X-RAY DIFFRACTION100
11.5148-29.99450.24291450.18812604X-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)
14.4266-1.2695-0.14235.87420.07545.49640.3240.16670.17990.3227-0.2893-0.3117-0.26930.1765-0.06841.2715-0.0382-0.01221.1574-0.1070.811961.905-29.4229-24.4749
24.0968-0.36031.46653.03680.88991.90680.0906-0.29250.20230.7031-0.51170.75240.3741-0.18370.08181.11310.08420.07780.99730.14711.090345.69-25.854-32.149
30.32230.87810.93443.4525-0.56421.8489-0.21630.16040.7396-1.84310.1039-0.09590.9950.4173-0.10091.79360.15620.16181.40710.0691.185550.1952-13.8297-69.206
42.25280.0243-0.45613.9846-0.08414.9971-0.33350.76011.3205-1.8247-0.96950.7412-2.46940.47221.01062.1755-0.1512-0.24641.92950.58963.094548.8314.8356-69.6229
54.4962-0.3834-2.69695.35920.16073.42220.23090.59830.1554-0.2695-0.34360.41761.75490.03120.27691.35590.19470.52811.4854-0.06481.141446.2502-23.463-54.3308
63.8217-0.36492.66926.4487-0.03155.1254-0.15260.01760.6685-0.32220.15720.4503-0.378-0.5097-0.12571.00770.0690.22661.49940.06331.579829.1953-2.2786-42.712
73.08391.8437-0.62268.8075-0.08886.2825-0.64570.53530.05591.00031.9872-0.3681-0.59980.0345-1.26750.89460.01880.01741.21240.03411.030838.2545-15.7548-35.3732
85.9255-2.3169-0.93982.8395-0.90722.8988-1.5087-2.7307-0.6761.59181.96990.42290.8550.4970.44371.26920.41090.13211.5944-0.20591.575148.6403-43.5223-41.887
96.79832.7429-1.17832.4479-0.27735.41180.70980.68981.24510.09140.1890.99630.8156-1.187-0.74930.9978-0.07690.01251.0810.00371.34431.9119-28.0252-45.6999
104.27592.87390.51979.00091.63875.7420.2737-0.2577-0.60080.8931-0.23-0.4949-0.07040.05-0.05731.00050.1821-0.07321.10080.17520.829258.890663.9552-22.6204
112.4323-0.3363-0.39490.92090.93922.86370.80291.0584-0.2865-0.1765-0.3168-0.48110.0147-0.0496-0.4751.7445-0.0285-0.32731.21320.01840.970556.111960.0553-40.0044
122.03222.0921-2.35584.4443-1.84862.1285-0.4493-1.35832.4885-1.0979-0.24643.40111.67940.16810.14521.4634-0.0174-0.1251.7593-0.09322.622420.026647.3165-44.4617
136.0067-0.8827-1.88694.1643-0.74461.2352.2305-0.5278-1.6451-0.3441-1.89191.75410.92060.1997-0.06382.988-0.1503-0.39791.66050.12652.32922.176328.1068-45.5242
144.8135-3.74230.0284.9113.2543.075-0.2713-0.9702-0.36-1.1986-0.25151.0608-0.5685-0.9250.32211.2213-0.12810.03541.40790.0821.70134.52957.5311-45.7493
155.5109-1.5591-0.54227.31760.1935.81-0.36710.8326-0.588-1.7433-0.18650.13241.0788-0.92340.40561.9861-0.11260.23231.4486-0.15171.069850.978536.4219-58.7154
166.30231.13430.84727.7054-2.13635.5043-1.75240.6228-0.3679-0.06832.3654-1.37820.629-1.0795-0.66461.4854-0.0672-0.20911.19540.03030.74955.410650.0553-48.2464
176.6021-0.0496-5.16223.34320.53748.25420.3956-2.42051.32441.39260.9648-0.72790.14682.4668-1.18432.14250.533-0.2521.8077-0.29421.338945.647277.725-40.2665
183.09361.3056-0.46172.2485-0.32393.656-0.86311.1123-0.3959-4.1668-0.37080.0155-0.7127-0.23890.57472.57430.04220.23341.32860.24490.884746.883362.1707-57.2799
194.58111.3724-0.73976.0279-2.22344.4662-0.0156-0.1105-0.3109-0.83480.3456-1.4696-0.19070.4779-0.21271.4832-0.22750.26461.4756-0.37061.732535.5005-40.4488-115.5661
204.60130.08520.16434.56270.82112.701-0.25041.02111.0541.1158-0.30880.10910.7361-0.28920.80970.7903-0.31450.2061.6051-0.1931.45918.3757-44.0911-110.4919
212.4161-0.05080.50571.7413-0.43241.36920.5071-1.1848-1.36581.8058-0.5979-0.839-0.6286-0.1287-0.37063.0302-0.0811-0.03472.02060.12211.487617.921-56.3811-73.943
221.63110.16882.64532.3627-0.90144.3152-0.217-0.70122.21091.0453-0.6198-0.65082.6385-0.07070.77272.26360.0381-0.07671.71980.21372.625515.9856-76.0092-75.4232
233.772.6211-1.90242.03231.10522.79180.8126-0.66420.83180.05120.26740.1408-1.46020.5288-0.76131.83360.0793-0.42391.7801-0.17811.876215.5321-46.3936-88.6012
242.93420.1073-2.91758.38170.56873.7699-0.2326-0.0645-0.355-0.46050.81131.97990.2534-0.9922-0.33550.7907-0.0672-0.25831.84660.15641.91850.562-67.8945-102.5543
252.0023-1.2775-0.94352.11490.15195.5897-1.0861-0.5514-0.19730.09842.5667-2.7498-0.3661-0.4478-1.53610.9208-0.12280.11131.3244-0.05391.722210.5058-54.3566-108.6113
261.43030.60021.43473.9791.045.3416-1.04490.2442-0.0152-1.16310.6176-1.8522-2.47740.1190.34651.7255-0.35420.25451.5523-0.38272.170819.5151-26.4129-100.6898
275.0232-0.22310.47534.3307-0.78695.89431.6252-0.1082-0.51580.6474-0.33733.7485-0.9812-0.5892-0.84391.07930.2880.02261.32020.03991.85452.4965-41.9882-99.2966
283.3847-3.0675-2.40665.3111.5572.4591-0.32920.46790.2342-0.88510.1882-1.6585-0.50880.09920.17091.5396-0.44560.16451.4395-0.06361.921733.20343.2263-117.7783
294.8913-1.6066-1.26133.95920.38744.70411.3499-1.1697-0.58880.1098-0.5121-2.1361-2.35780.4704-1.07431.6412-0.36170.09731.55850.05111.81127.94236.9787-100.9284
300.06270.4385-0.13141.2416-0.31610.4343-0.95241.6136-1.73570.68780.13663.679-0.1879-0.95910.6631.39130.26630.33642.38360.02973.2352-8.441220.3449-101.0362
315.15510.4614-2.5893.9828-0.5273.26121.6565-0.9930.1829-0.2383-2.3263-1.807-1.79680.38130.29582.6626-0.02160.32931.9610.2332.0056-6.216439.3-98.7641
324.5981-1.81641.26252.41370.7914.2661-1.14961.3572-0.31661.18180.6569-0.270.4311-0.49330.66921.5868-0.3014-0.03191.58180.20461.11785.89169.7093-97.609
333.8417-0.0592-2.14934.77190.77782.40750.1035-0.85340.48050.9271-0.0371-1.0001-0.8318-0.10990.02792.10520.1671-0.72321.75630.06542.198320.624530.5844-82.7778
347.3044-0.51351.01065.33771.49017.453-0.3574-0.57070.1856-2.38921.33090.84390.18860.0765-1.15810.9910.06580.06391.12870.10141.019826.429517.268-92.9417
355.25550.3574.16664.55532.11098.4709-0.10781.77871.03830.06850.2484-1.40251.64332.1739-0.27381.6352-0.21690.10181.98740.18342.045717.3533-10.5159-102.0899
363.7706-0.15312.19684.31511.08762.437-0.6753-0.5777-0.76592.33380.10940.0285-0.5637-0.44760.36882.0245-0.07050.08691.58950.41611.631916.93975.0679-85.0724
372.06961.3852-1.42552.38191.22312.3677-0.59570.51891.03711.357-0.1448-1.2762-1.19491.19630.79582.0862-0.15080.05661.73060.29092.173856.00350.7371-45.988
382.79110.36031.86222.0333-0.98621.6097-0.1819-0.05650.00890.3840.3877-0.3638-0.95680.0216-0.1041.99320.3840.05851.8111-0.04371.625555.9557-3.3397-48.3831
396.60960.88261.96474.2535-0.6520.9702-2.4718-1.38690.16361.24462.10831.43853.5802-1.39180.38532.9460.10420.43171.84340.29141.740837.056435.9713-32.8021
404.3162-0.84030.88944.66882.94977.1888-1.4056-0.71650.36980.8509-0.35652.42511.156-1.82232.52172.4076-0.0475-0.25911.4212-0.3262.821633.734839.3696-32.6819
412.15260.21.67040.47810.37310.8018-0.6082-1.0394-1.92390.7260.6292-0.96380.09511.047-0.10951.7250.1689-0.12452.27280.10222.198127.723-69.4481-90.8628
424.1908-1.115-0.18425.5034-0.84351.8119-0.87960.01550.551-0.80420.4314-1.44791.4894-0.10050.05491.7097-0.00190.02581.8482-0.11831.784926.6859-65.3947-88.6401
432.5624-0.65570.03721.2119-0.83130.53630.03660.257-0.4709-1.79121.22061.26-1.2904-0.8782-1.03622.6755-0.1675-0.47531.79580.32312.18329.578331.8463-110.1724
441.678-0.4195-2.86771.07240.64444.5127-0.3320.8713-1.1488-0.8056-0.1313-0.94930.1676-0.81020.35942.5226-0.07510.26132.0654-0.07542.09466.62828.3947-110.4457
450.0080.1095-0.12511.6686-1.7631.86060.0164-1.3624-0.22460.32.17360.40160.29-0.1332-0.2868-4.48170.54510.35182.60371.30933.907733.2009-12.6942-47.2175
462.41840.5441.08730.5133-0.80043.35621.2026-1.24270.26860.3312-0.6492-0.33390.3663-1.0156-0.12394.1885-2.49531.42921.6018-2.88760.865745.013747.1979-56.4844
473.6022-1.0921-1.76141.3721.6374.3889-0.3530.66060.7965-1.14511.39681.0244-1.91321.6589-0.1461.7676-0.51260.13691.82260.29072.36253.8563-57.3231-97.507
482.61090.70080.23910.857-0.79331.1232-1.75190.53040.06760.42260.59560.3810.16460.51280.95154.33571.25590.21492.03361.13131.273615.309520.3144-85.8987
49-0.12770.0202-0.3742-0.10181.1649-2.17550.1637-0.15690.0817-0.1534-0.58410.31771.7959-0.4470.07310.4937-0.0752-0.41852.19140.34190.811233.9227-0.6557-70.9718
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 C AND RESID 1824:2068 )C1824 - 2068
24X-RAY DIFFRACTION20( CHAIN C AND RESID 2069:2092 )C2069 - 2092
25X-RAY DIFFRACTION21( CHAIN C AND ( RESID 2093:2124 OR RESID 2192:2217 ) )C2093 - 2124
26X-RAY DIFFRACTION21( CHAIN C AND ( RESID 2093:2124 OR RESID 2192:2217 ) )C2192 - 2217
27X-RAY DIFFRACTION22( CHAIN C AND RESID 2125:2191 )C2125 - 2191
28X-RAY DIFFRACTION23( CHAIN C AND RESID 2218:2323 )C2218 - 2323
29X-RAY DIFFRACTION24( CHAIN C AND RESID 2332:2459 )C2332 - 2459
30X-RAY DIFFRACTION25( CHAIN C AND RESID 2460:2495 )C2460 - 2495
31X-RAY DIFFRACTION26( CHAIN C AND RESID 2496:2532 )C2496 - 2532
32X-RAY DIFFRACTION27( CHAIN C AND ( RESID 2324:2331 OR RESID 2533:2590 ) )C2324 - 2331
33X-RAY DIFFRACTION27( CHAIN C AND ( RESID 2324:2331 OR RESID 2533:2590 ) )C2533 - 2590
34X-RAY DIFFRACTION28( CHAIN D AND RESID 1824:2068 )D1824 - 2068
35X-RAY DIFFRACTION29( CHAIN D AND RESID 2069:2092 )D2069 - 2092
36X-RAY DIFFRACTION30( CHAIN D AND ( RESID 2093:2124 OR RESID 2192:2217 ) )D2093 - 2124
37X-RAY DIFFRACTION30( CHAIN D AND ( RESID 2093:2124 OR RESID 2192:2217 ) )D2192 - 2217
38X-RAY DIFFRACTION31( CHAIN D AND RESID 2125:2191 )D2125 - 2191
39X-RAY DIFFRACTION32( CHAIN D AND RESID 2218:2323 )D2218 - 2323
40X-RAY DIFFRACTION33( CHAIN D AND RESID 2332:2459 )D2332 - 2459
41X-RAY DIFFRACTION34( CHAIN D AND RESID 2460:2495 )D2460 - 2495
42X-RAY DIFFRACTION35( CHAIN D AND RESID 2496:2532 )D2496 - 2532
43X-RAY DIFFRACTION36( CHAIN D AND ( RESID 2324:2331 OR RESID 2533:2590 ) )D2324 - 2331
44X-RAY DIFFRACTION36( CHAIN D AND ( RESID 2324:2331 OR RESID 2533:2590 ) )D2533 - 2590
45X-RAY DIFFRACTION37( CHAIN E AND RESID 1:18 )E1 - 18
46X-RAY DIFFRACTION38( CHAIN F AND RESID 2:13 )F2 - 13
47X-RAY DIFFRACTION39( CHAIN G AND RESID 1:18 )G1 - 18
48X-RAY DIFFRACTION40( CHAIN H AND RESID 1:13 )H1 - 13
49X-RAY DIFFRACTION41( CHAIN I AND RESID 1:18 )I1 - 18
50X-RAY DIFFRACTION42( CHAIN J AND RESID 2:13 )J2 - 13
51X-RAY DIFFRACTION43( CHAIN K AND RESID 1:18 )K1 - 18
52X-RAY DIFFRACTION44( CHAIN L AND RESID 1:13 )L1 - 13
53X-RAY DIFFRACTION45( CHAIN A AND RESID 2603:2604 )A2603 - 2604
54X-RAY DIFFRACTION46( CHAIN B AND RESID 2603:2604 )B2603 - 2604
55X-RAY DIFFRACTION47( CHAIN C AND RESID 2604:2604 )C2604
56X-RAY DIFFRACTION48( CHAIN D AND RESID 2604:2604 )D2604
57X-RAY DIFFRACTION49( CHAIN A AND RESID 2601:2602 ) OR ( CHAIN C AND RESID 2601:2603 ) OR ( CHAIN B AND RESID 2601:2602 ) OR ( CHAIN D AND RESID 2601:2603 )A2601 - 2602
58X-RAY DIFFRACTION49( CHAIN A AND RESID 2601:2602 ) OR ( CHAIN C AND RESID 2601:2603 ) OR ( CHAIN B AND RESID 2601:2602 ) OR ( CHAIN D AND RESID 2601:2603 )C2601 - 2603
59X-RAY DIFFRACTION49( CHAIN A AND RESID 2601:2602 ) OR ( CHAIN C AND RESID 2601:2603 ) OR ( CHAIN B AND RESID 2601:2602 ) OR ( CHAIN D AND RESID 2601:2603 )B2601 - 2602
60X-RAY DIFFRACTION49( CHAIN A AND RESID 2601:2602 ) OR ( CHAIN C AND RESID 2601:2603 ) OR ( CHAIN B AND RESID 2601:2602 ) OR ( CHAIN D AND RESID 2601:2603 )D2601 - 2603

+
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