[English] 日本語
Yorodumi
- PDB-3olb: Poliovirus polymerase elongation complex with 2',3'-dideoxy-ctp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3olb
TitlePoliovirus polymerase elongation complex with 2',3'-dideoxy-ctp
Components
  • Polymerase
  • RNA (5'-R(*AP*AP*GP*UP*CP*U*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*CP*GP*GP*AP*AP*A)-3')
  • RNA (5'-R(*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
  • RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
KeywordsTRANSFERASE/RNA / RNA-dependent RNA polymerase / elongation complex / virus / protein-RNA complex / TRANSFERASE-RNA complex
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Reverse transcriptase/Diguanylate cyclase domain / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A ...Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Reverse transcriptase/Diguanylate cyclase domain / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE / ISOPROPYL ALCOHOL / RNA / RNA (> 10) / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsGong, P. / Peersen, O.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase.
Authors: Gong, P. / Peersen, O.B.
History
DepositionAug 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polymerase
B: RNA (5'-R(*AP*AP*GP*UP*CP*U*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*CP*GP*GP*AP*AP*A)-3')
C: RNA (5'-R(*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
D: RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
E: Polymerase
F: RNA (5'-R(*AP*AP*GP*UP*CP*U*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*CP*GP*GP*AP*AP*A)-3')
G: RNA (5'-R(*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
H: RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
I: Polymerase
J: RNA (5'-R(*AP*AP*GP*UP*CP*U*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*CP*GP*GP*AP*AP*A)-3')
K: RNA (5'-R(*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
L: RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
M: Polymerase
N: RNA (5'-R(*AP*AP*GP*UP*CP*U*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*CP*GP*GP*AP*AP*A)-3')
O: RNA (5'-R(*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
P: RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,10736
Polymers278,31916
Non-polymers2,78720
Water16,177898
1
A: Polymerase
B: RNA (5'-R(*AP*AP*GP*UP*CP*U*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*CP*GP*GP*AP*AP*A)-3')
C: RNA (5'-R(*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
D: RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2178
Polymers69,5804
Non-polymers6374
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Polymerase
F: RNA (5'-R(*AP*AP*GP*UP*CP*U*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*CP*GP*GP*AP*AP*A)-3')
G: RNA (5'-R(*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
H: RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,33710
Polymers69,5804
Non-polymers7576
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Polymerase
J: RNA (5'-R(*AP*AP*GP*UP*CP*U*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*CP*GP*GP*AP*AP*A)-3')
K: RNA (5'-R(*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
L: RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2779
Polymers69,5804
Non-polymers6975
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: Polymerase
N: RNA (5'-R(*AP*AP*GP*UP*CP*U*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*CP*GP*GP*AP*AP*A)-3')
O: RNA (5'-R(*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
P: RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2779
Polymers69,5804
Non-polymers6975
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.528, 60.539, 192.936
Angle α, β, γ (deg.)83.82, 83.84, 77.35
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26
17
27
18
28

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A
211chain E
112chain I
212chain M
113chain B
213chain F
114chain J
214chain N
115chain C
215chain G
116chain K
216chain O
117chain D
217chain H
118chain L
218chain P

NCS ensembles :
ID
1
2
3
4
5
6
7
8

-
Components

-
Protein , 1 types, 4 molecules AEIM

#1: Protein
Polymerase


Mass: 53761.195 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 1749-2209 / Mutation: L446D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Strain: Mahoney / Gene: 3D / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3VQP5, RNA-directed RNA polymerase

-
RNA chain , 3 types, 12 molecules BFJNCGKODHLP

#2: RNA chain
RNA (5'-R(*AP*AP*GP*UP*CP*U*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*CP*GP*GP*AP*AP*A)-3')


Mass: 8279.961 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: RNA prepared by T7 RNA polymerase transcription followed by glmS ribozyme self-cleavage
#3: RNA chain
RNA (5'-R(*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')


Mass: 4563.828 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: 5' portion was generated by chemical synthesis. The 3'-tetranucleotide was added to the RNA chain by poliovirus RNA-dependent RNA polymerase
#4: RNA chain
RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')


Mass: 2974.854 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: RNA prepared by T7 RNA polymerase transcription followed by glmS ribozyme self-cleavage

-
Non-polymers , 4 types, 918 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-DCT / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE


Type: DNA linking / Mass: 451.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H16N3O12P3
#7: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 898 / 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: 2.45 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 95 mM trisodium citrate, pH 5.6-5.9, 6.5-7.0% (v/v) isopropanol, 16.5-18.0% (w/v) PEG4000, 5% (v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 283K
PH range: 5.6-5.9

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Dec 8, 2009
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→45.23 Å / Num. obs: 149534 / % possible obs: 96.8 % / Redundancy: 1.97 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 4.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.85 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 1 / % possible all: 94.5

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RA6

1ra6


Resolution: 2.41→45.226 Å / SU ML: 0.5 / σ(F): 2.06 / Phase error: 36.09 / Stereochemistry target values: ML
Details: WHILE STRUCTURE FACTOR FILE CONTAINS DATA TO 2.10 A RESOLUTION, DATA WERE REFINED TO 2.41 A
RfactorNum. reflection% reflection
Rfree0.2613 4981 5.03 %
Rwork0.2173 --
obs0.2196 98983 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.498 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.3597 Å23.1097 Å25.3705 Å2
2--3.3391 Å2-2.3024 Å2
3----10.6989 Å2
Refinement stepCycle: LAST / Resolution: 2.41→45.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14788 3014 160 898 18860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818660
X-RAY DIFFRACTIONf_angle_d1.06325938
X-RAY DIFFRACTIONf_dihedral_angle_d16.6597348
X-RAY DIFFRACTIONf_chiral_restr0.0682928
X-RAY DIFFRACTIONf_plane_restr0.0052752
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3698X-RAY DIFFRACTIONPOSITIONAL
12E3698X-RAY DIFFRACTIONPOSITIONAL0.024
21I3698X-RAY DIFFRACTIONPOSITIONAL
22M3698X-RAY DIFFRACTIONPOSITIONAL0.03
31B361X-RAY DIFFRACTIONPOSITIONAL
32F361X-RAY DIFFRACTIONPOSITIONAL0.02
41J381X-RAY DIFFRACTIONPOSITIONAL
42N381X-RAY DIFFRACTIONPOSITIONAL0.019
51C303X-RAY DIFFRACTIONPOSITIONAL
52G303X-RAY DIFFRACTIONPOSITIONAL0.019
61K303X-RAY DIFFRACTIONPOSITIONAL
62O303X-RAY DIFFRACTIONPOSITIONAL0.019
71D68X-RAY DIFFRACTIONPOSITIONAL
72H68X-RAY DIFFRACTIONPOSITIONAL0.006
81L91X-RAY DIFFRACTIONPOSITIONAL
82P91X-RAY DIFFRACTIONPOSITIONAL0.007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.43740.49751620.40723084X-RAY DIFFRACTION96
2.4374-2.46610.44011670.4063043X-RAY DIFFRACTION97
2.4661-2.49610.37261630.35353134X-RAY DIFFRACTION97
2.4961-2.52770.34441670.34373210X-RAY DIFFRACTION97
2.5277-2.5610.42451590.37913059X-RAY DIFFRACTION97
2.561-2.59610.43421600.373138X-RAY DIFFRACTION97
2.5961-2.63310.39091740.34863238X-RAY DIFFRACTION97
2.6331-2.67240.41191780.34853011X-RAY DIFFRACTION97
2.6724-2.71420.44541490.33963188X-RAY DIFFRACTION97
2.7142-2.75870.43711460.32873196X-RAY DIFFRACTION97
2.7587-2.80630.40621470.31013080X-RAY DIFFRACTION97
2.8063-2.85730.33811470.28793182X-RAY DIFFRACTION97
2.8573-2.91220.36651680.2683152X-RAY DIFFRACTION97
2.9122-2.97170.34751410.25473087X-RAY DIFFRACTION97
2.9717-3.03630.30181790.2423242X-RAY DIFFRACTION98
3.0363-3.10690.30011740.24053053X-RAY DIFFRACTION97
3.1069-3.18450.29291870.23193216X-RAY DIFFRACTION97
3.1845-3.27060.29061610.22733090X-RAY DIFFRACTION97
3.2706-3.36680.26881960.21443210X-RAY DIFFRACTION98
3.3668-3.47550.22921780.21153033X-RAY DIFFRACTION97
3.4755-3.59960.27241720.20233196X-RAY DIFFRACTION97
3.5996-3.74370.21541700.17663112X-RAY DIFFRACTION97
3.7437-3.9140.23161790.16973151X-RAY DIFFRACTION98
3.914-4.12020.20281660.14573152X-RAY DIFFRACTION98
4.1202-4.37820.16821640.13533183X-RAY DIFFRACTION98
4.3782-4.71590.16461580.13153216X-RAY DIFFRACTION98
4.7159-5.18980.191580.15683126X-RAY DIFFRACTION98
5.1898-5.93940.22621770.22893166X-RAY DIFFRACTION97
5.9394-7.47750.30991790.28473142X-RAY DIFFRACTION97
7.4775-45.23370.25031550.22122912X-RAY DIFFRACTION91
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)
10.5779-0.4178-0.20590.38940.44950.46310.0737-0.4651-0.11920.22120.14420.1446-0.0892-0.8236-00.4959-0.0636-0.02860.71170.07710.379212.831218.2248132.0615
20.60610.39210.42680.31960.23650.49310.00910.06370.0974-0.2487-0.0511-0.1186-0.2619-0.006500.44540.0286-0.05080.3235-0.02230.372733.24932.9368132.7188
30.5981-0.42710.4530.7388-0.05020.7719-0.00180.0761-0.0201-0.1166-0.0075-0.07510.0231-0.1876-00.38140.0106-0.05410.338-0.00640.354122.535218.8883100.2345
40.61030.136-0.20251.79790.39411.05530.0199-0.0375-0.03730.14210.0264-0.09810.1477-0.013900.40920.0228-0.03880.3210.00660.350534.79824.7715124.5849
50.3467-0.11560.26790.5773-0.17140.7161-0.03790.21050.1138-0.41360.2789-0.2161-0.91690.3436-00.718-0.11740.05730.5154-0.06640.40173.623966.876464.961
60.13030.24980.32530.42540.47180.7965-0.1168-0.1442-0.10980.06880.06440.2957-0.2569-0.43600.39480.0588-0.02150.4635-0.020.368254.805650.171264.3051
70.7324-0.57020.12290.62160.4540.8221-0.0563-0.1463-0.02690.08510.08140.0355-0.18570.018900.354-0.00420.00760.3527-0.04130.345970.84657.558996.7895
81.4698-0.0130.18080.5896-0.39971.1522-0.00690.0519-0.1124-0.05690.0092-0.0603-0.06950.1281-00.36170.05210.00630.3868-0.05380.377981.942642.499172.4441
90.4672-0.421-0.29770.52720.18270.53450.0506-0.106-0.0417-0.0010.11350.0891-0.1332-0.567100.4278-0.020.00620.63040.02130.393735.400945.028636.7046
100.62540.26340.3680.2755-0.04040.3317-0.01450.11990.0446-0.037-0.0577-0.2453-0.30040.1626-00.51070.038-0.02780.3725-0.01720.37455.961259.291237.0184
111.3658-0.8210.72160.72810.24280.97020.06710.19950.0472-0.2414-0.095-0.1048-0.0165-0.1952-00.41420.0276-0.04010.33580.03060.380445.087445.09054.7452
120.55960.4032-0.03271.47930.56691.21190.0392-0.0405-0.03720.0907-0.0376-0.08480.2441-0.014100.3710.0254-0.04420.26990.01770.314857.363130.916829.0805
130.2415-0.39470.15910.462-0.08520.60470.0816-0.01520.0934-0.13960.1168-0.1556-0.70010.0918-00.7297-0.0870.03590.4636-0.02810.441795.586693.1889-30.7762
140.0470.1749-0.01060.56950.28410.4935-0.0802-0.0149-0.10630.05910.10760.2673-0.1451-0.4791-00.43370.0498-0.01510.4964-0.00530.402377.175976.2461-31.0882
150.4823-0.69920.16561.02620.67181.1448-0.0851-0.2083-0.07250.10660.12750.1246-0.2902-0.0576-00.35080.02410.01840.3498-0.04650.358793.401883.76071.1854
161.38280.16180.23510.4994-0.20591.2141-0.04520.0891-0.1134-0.05690.029-0.0396-0.03170.190400.31420.04280.01740.3596-0.0570.3543104.546868.6738-23.1451
170.01220.00920.0040.01720.0160.0077-0.42030.3416-0.2511-0.1792-0.31480.228-0.6927-0.0822-01.15420.1585-0.19830.74580.03670.62415.274536.1754125.5933
180.8125-0.06290.36211.12880.88980.7283-0.1612-0.03080.0647-0.38550.1885-0.0889-0.05210.1284-00.5031-0.08140.08270.37290.02070.457834.546329.5784111.1362
190.0098-0.012-0.00570.0072-0.00270.0032-0.3068-0.50220.38510.0542-0.4057-0.3711-0.1765-0.1906-00.89810.2659-0.05011.0095-0.21190.65555.570268.40971.4106
201.3173-0.2431.12790.86150.29381.18820.0811-0.3181-0.01810.0521-0.05760.16160.1573-0.104600.3967-0.04790.08220.46530.03590.465557.812848.182385.8965
210.010.0018-0.02020.00640.00570.0198-0.39210.10080.2216-0.1624-0.50540.2193-0.31010.1346-01.32540.2237-0.16040.7257-0.13450.83237.810262.403529.7226
220.7688-0.17540.4310.91320.52020.5771-0.11710.02980.1055-0.36530.1179-0.1803-0.17380.164200.4794-0.09020.07460.35330.04850.427657.173655.733515.5826
230.0056-0.0093-0.00710.0052-0.01230.012-0.6055-0.0880.41380.0508-0.2204-0.1694-0.21090.0229-01.05060.3904-0.1550.99-0.01240.857378.091994.6147-23.8392
241.1547-0.36140.73221.00570.52050.9937-0.0117-0.3863-0.09580.0265-0.03130.11970.2953-0.26400.4356-0.08050.09150.50020.02470.463980.381874.2865-9.6533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 1:25 or resid 39:65 or resid 153:180 or resid 269:284)
2X-RAY DIFFRACTION2chain A and resid 102:152
3X-RAY DIFFRACTION3chain A and (resid 26:38 or resid 369:461)
4X-RAY DIFFRACTION4chain A and (resid 66:101 or resid 181:268 or resid 285:368)
5X-RAY DIFFRACTION5chain E and (resid 1:25 or resid 39:65 or resid 153:180 or resid 269:284)
6X-RAY DIFFRACTION6chain E and resid 102:152
7X-RAY DIFFRACTION7chain E and (resid 26:38 or resid 369:461)
8X-RAY DIFFRACTION8chain E and (resid 66:101 or resid 181:268 or resid 285:368)
9X-RAY DIFFRACTION9chain I and (resid 1:25 or resid 39:65 or resid 153:180 or resid 269:284)
10X-RAY DIFFRACTION10chain I and resid 102:152
11X-RAY DIFFRACTION11chain I and (resid 26:38 or resid 369:461)
12X-RAY DIFFRACTION12chain I and (resid 66:101 or resid 181:268 or resid 285:368)
13X-RAY DIFFRACTION13chain M and (resid 1:25 or resid 39:65 or resid 153:180 or resid 269:284)
14X-RAY DIFFRACTION14chain M and resid 102:152
15X-RAY DIFFRACTION15chain M and (resid 26:38 or resid 369:461)
16X-RAY DIFFRACTION16chain M and (resid 66:101 or resid 181:268 or resid 285:368)
17X-RAY DIFFRACTION17(chain B and resid 595:599) or (chain D and resid 1:4)
18X-RAY DIFFRACTION18(chain B and resid 600:613) or (chain C and resid 688:702)
19X-RAY DIFFRACTION19(chain F and resid 595:599) or (chain H and resid 1:4)
20X-RAY DIFFRACTION20(chain F and resid 600:613) or (chain G and resid 688:702)
21X-RAY DIFFRACTION21(chain J and resid 596:599) or (chain L and resid 1:3)
22X-RAY DIFFRACTION22(chain J and resid 600:613) or (chain K and resid 688:702)
23X-RAY DIFFRACTION23(chain N and resid 596:599) or (chain P and resid 1:3)
24X-RAY DIFFRACTION24(chain N and resid 600:613) or (chain O and resid 688:702)

+
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