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- PDB-8aff: Wild type oxalyl-CoA synthetase Pcs60p -

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Basic information

Entry
Database: PDB / ID: 8aff
TitleWild type oxalyl-CoA synthetase Pcs60p
ComponentsOxalate--CoA ligase
KeywordsLIGASE / Peroxisome / Oxalyl-CoA ligase / Oligomer / Yeast
Function / homology
Function and homology information


oxalate-CoA ligase / oxalate-CoA ligase activity / medium-chain fatty acid-CoA ligase activity / oxalate catabolic process / peroxisomal membrane / peroxisomal matrix / fatty acid metabolic process / mRNA binding / ATP binding / cytoplasm
Similarity search - Function
Oxalate--CoA ligase Pcs60-like / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsBurgi, J. / Chojnowski, G. / Giannopoulou, E.A. / Wilmanns, M.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)1058/9-1 Germany
German Research Foundation (DFG)1058/9-2 Germany
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND664726 Germany
CitationJournal: Biol Chem / Year: 2023
Title: Asymmetric horseshoe-like assembly of peroxisomal yeast oxalyl-CoA synthetase.
Authors: Jérôme Bürgi / Pascal Lill / Evdokia-Anastasia Giannopoulou / Cy M Jeffries / Grzegorz Chojnowski / Stefan Raunser / Christos Gatsogiannis / Matthias Wilmanns /
Abstract: Oxalyl-CoA synthetase from is one of the most abundant peroxisomal proteins in yeast and hence has become a model to study peroxisomal translocation. It contains a C-terminal Peroxisome Targeting ...Oxalyl-CoA synthetase from is one of the most abundant peroxisomal proteins in yeast and hence has become a model to study peroxisomal translocation. It contains a C-terminal Peroxisome Targeting Signal 1, which however is partly dispensable, suggesting additional receptor bindings sites. To unravel any additional features that may contribute to its capacity to be recognized as peroxisomal target, we determined its assembly and overall architecture by an integrated structural biology approach, including X-ray crystallography, single particle cryo-electron microscopy and small angle X-ray scattering. Surprisingly, it assembles into mixture of concentration-dependent dimers, tetramers and hexamers by dimer self-association. Hexameric particles form an unprecedented asymmetric horseshoe-like arrangement, which considerably differs from symmetric hexameric assembly found in many other protein structures. A single mutation within the self-association interface is sufficient to abolish any higher-level oligomerization, resulting in a homogenous dimeric assembly. The small C-terminal domain of yeast Oxalyl-CoA synthetase is connected by a partly flexible hinge with the large N-terminal domain, which provides the sole basis for oligomeric assembly. Our data provide a basis to mechanistically study peroxisomal translocation of this target.
History
DepositionJul 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxalate--CoA ligase
B: Oxalate--CoA ligase
C: Oxalate--CoA ligase
D: Oxalate--CoA ligase
E: Oxalate--CoA ligase
F: Oxalate--CoA ligase
G: Oxalate--CoA ligase
H: Oxalate--CoA ligase
I: Oxalate--CoA ligase
J: Oxalate--CoA ligase
K: Oxalate--CoA ligase
L: Oxalate--CoA ligase


Theoretical massNumber of molelcules
Total (without water)726,74912
Polymers726,74912
Non-polymers00
Water5,711317
1
A: Oxalate--CoA ligase


  • defined by author
  • Evidence: SAXS, Concentration dependent oligomerization. We used OLIGOMER to estimate the volume fraction of each oligomeric state depending on the protein concentration analyzed., electron ...Evidence: SAXS, Concentration dependent oligomerization. We used OLIGOMER to estimate the volume fraction of each oligomeric state depending on the protein concentration analyzed., electron microscopy, The Cryogenic electron microscopy structure of Pcs60 showed the formation of hexameric homooligomers, light scattering, Multi angle light scattering at different protein concentration showed formation of mixed population of homooligomeric complexes.
  • 60.6 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)60,5621
Polymers60,5621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oxalate--CoA ligase


Theoretical massNumber of molelcules
Total (without water)60,5621
Polymers60,5621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Oxalate--CoA ligase


Theoretical massNumber of molelcules
Total (without water)60,5621
Polymers60,5621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Oxalate--CoA ligase


Theoretical massNumber of molelcules
Total (without water)60,5621
Polymers60,5621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Oxalate--CoA ligase


Theoretical massNumber of molelcules
Total (without water)60,5621
Polymers60,5621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Oxalate--CoA ligase


Theoretical massNumber of molelcules
Total (without water)60,5621
Polymers60,5621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Oxalate--CoA ligase


Theoretical massNumber of molelcules
Total (without water)60,5621
Polymers60,5621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Oxalate--CoA ligase


Theoretical massNumber of molelcules
Total (without water)60,5621
Polymers60,5621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Oxalate--CoA ligase


Theoretical massNumber of molelcules
Total (without water)60,5621
Polymers60,5621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Oxalate--CoA ligase


Theoretical massNumber of molelcules
Total (without water)60,5621
Polymers60,5621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Oxalate--CoA ligase


Theoretical massNumber of molelcules
Total (without water)60,5621
Polymers60,5621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Oxalate--CoA ligase


Theoretical massNumber of molelcules
Total (without water)60,5621
Polymers60,5621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.029, 93.724, 356.488
Angle α, β, γ (deg.)90.000, 93.811, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53A
63D
74A
84E
95A
105F
116A
126G
137A
147H
158A
168I
179A
189J
1910A
2010K
2111A
2211L
2312B
2412C
2513B
2613D
2714B
2814E
2915B
3015F
3116B
3216G
3317B
3417H
3518B
3618I
3719B
3819J
3920B
4020K
4121B
4221L
4322C
4422D
4523C
4623E
4724C
4824F
4925C
5025G
5126C
5226H
5327C
5427I
5528C
5628J
5729C
5829K
5930C
6030L
6131D
6231E
6332D
6432F
6533D
6633G
6734D
6834H
6935D
7035I
7136D
7236J
7337D
7437K
7538D
7638L
7739E
7839F
7940E
8040G
8141E
8241H
8342E
8442I
8543E
8643J
8744E
8844K
8945E
9045L
9146F
9246G
9347F
9447H
9548F
9648I
9749F
9849J
9950F
10050K
10151F
10251L
10352G
10452H
10553G
10653I
10754G
10854J
10955G
11055K
11156G
11256L
11357H
11457I
11558H
11658J
11759H
11859K
11960H
12060L
12161I
12261J
12362I
12462K
12563I
12663L
12764J
12864K
12965J
13065L
13166K
13266L

NCS domain segments:

Beg auth comp-ID: ALA / Beg label comp-ID: ALA

Dom-IDComponent-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUAA9 - 4359 - 435
221GLUGLUBB9 - 4359 - 435
332ILEILEAA9 - 4379 - 437
442ILEILECC9 - 4379 - 437
553LYSLYSAA9 - 5189 - 518
663LYSLYSDD9 - 5189 - 518
774ILEILEAA9 - 4339 - 433
884ILEILEEE9 - 4339 - 433
995LEULEUAA9 - 4369 - 436
10105LEULEUFF9 - 4369 - 436
11116THRTHRAA9 - 4309 - 430
12126THRTHRGG9 - 4309 - 430
13137LYSLYSAA9 - 4349 - 434
14147LYSLYSHH9 - 4349 - 434
15158THRTHRAA9 - 5329 - 532
16168THRTHRII9 - 5329 - 532
17179LYSLYSAA9 - 4349 - 434
18189LYSLYSJJ9 - 4349 - 434
191910ARGARGAA9 - 4329 - 432
202010ARGARGKK9 - 4329 - 432
212111ILEILEAA9 - 4339 - 433
222211ILEILELL9 - 4339 - 433
232312GLUGLUBB9 - 4359 - 435
242412GLUGLUCC9 - 4359 - 435
252513GLUGLUBB9 - 4359 - 435
262613GLUGLUDD9 - 4359 - 435
272714ILEILEBB9 - 4339 - 433
282814ILEILEEE9 - 4339 - 433
292915GLUGLUBB9 - 4359 - 435
303015GLUGLUFF9 - 4359 - 435
313116THRTHRBB9 - 4309 - 430
323216THRTHRGG9 - 4309 - 430
333317LYSLYSBB9 - 4349 - 434
343417LYSLYSHH9 - 4349 - 434
353518GLUGLUBB9 - 4359 - 435
363618GLUGLUII9 - 4359 - 435
373719LYSLYSBB9 - 4349 - 434
383819LYSLYSJJ9 - 4349 - 434
393920ARGARGBB9 - 4329 - 432
404020ARGARGKK9 - 4329 - 432
414121ILEILEBB9 - 4339 - 433
424221ILEILELL9 - 4339 - 433
434322ILEILECC9 - 4379 - 437
444422ILEILEDD9 - 4379 - 437
454523ILEILECC9 - 4339 - 433
464623ILEILEEE9 - 4339 - 433
474724LEULEUCC9 - 4369 - 436
484824LEULEUFF9 - 4369 - 436
494925THRTHRCC9 - 4309 - 430
505025THRTHRGG9 - 4309 - 430
515126LYSLYSCC9 - 4349 - 434
525226LYSLYSHH9 - 4349 - 434
535327ILEILECC9 - 4379 - 437
545427ILEILEII9 - 4379 - 437
555528LYSLYSCC9 - 4349 - 434
565628LYSLYSJJ9 - 4349 - 434
575729ARGARGCC9 - 4329 - 432
585829ARGARGKK9 - 4329 - 432
595930ILEILECC9 - 4339 - 433
606030ILEILELL9 - 4339 - 433
616131ILEILEDD9 - 4339 - 433
626231ILEILEEE9 - 4339 - 433
636332LEULEUDD9 - 4369 - 436
646432LEULEUFF9 - 4369 - 436
656533THRTHRDD9 - 4309 - 430
666633THRTHRGG9 - 4309 - 430
676734LYSLYSDD9 - 4349 - 434
686834LYSLYSHH9 - 4349 - 434
696935LYSLYSDD9 - 5189 - 518
707035LYSLYSII9 - 5189 - 518
717136LYSLYSDD9 - 4349 - 434
727236LYSLYSJJ9 - 4349 - 434
737337ARGARGDD9 - 4329 - 432
747437ARGARGKK9 - 4329 - 432
757538ILEILEDD9 - 4339 - 433
767638ILEILELL9 - 4339 - 433
777739ILEILEEE9 - 4339 - 433
787839ILEILEFF9 - 4339 - 433
797940THRTHREE9 - 4309 - 430
808040THRTHRGG9 - 4309 - 430
818141ILEILEEE9 - 4339 - 433
828241ILEILEHH9 - 4339 - 433
838342ILEILEEE9 - 4339 - 433
848442ILEILEII9 - 4339 - 433
858543ILEILEEE9 - 4339 - 433
868643ILEILEJJ9 - 4339 - 433
878744ARGARGEE9 - 4329 - 432
888844ARGARGKK9 - 4329 - 432
898945LYSLYSEE9 - 4349 - 434
909045LYSLYSLL9 - 4349 - 434
919146THRTHRFF9 - 4309 - 430
929246THRTHRGG9 - 4309 - 430
939347LYSLYSFF9 - 4349 - 434
949447LYSLYSHH9 - 4349 - 434
959548LEULEUFF9 - 4369 - 436
969648LEULEUII9 - 4369 - 436
979749LYSLYSFF9 - 4349 - 434
989849LYSLYSJJ9 - 4349 - 434
999950ARGARGFF9 - 4329 - 432
10010050ARGARGKK9 - 4329 - 432
10110151ILEILEFF9 - 4339 - 433
10210251ILEILELL9 - 4339 - 433
10310352THRTHRGG9 - 4309 - 430
10410452THRTHRHH9 - 4309 - 430
10510553THRTHRGG9 - 4309 - 430
10610653THRTHRII9 - 4309 - 430
10710754THRTHRGG9 - 4309 - 430
10810854THRTHRJJ9 - 4309 - 430
10910955THRTHRGG9 - 4309 - 430
11011055THRTHRKK9 - 4309 - 430
11111156THRTHRGG9 - 4309 - 430
11211256THRTHRLL9 - 4309 - 430
11311357LYSLYSHH9 - 4349 - 434
11411457LYSLYSII9 - 4349 - 434
11511558GLUGLUHH9 - 4359 - 435
11611658GLUGLUJJ9 - 4359 - 435
11711759ARGARGHH9 - 4329 - 432
11811859ARGARGKK9 - 4329 - 432
11911960ILEILEHH9 - 4339 - 433
12012060ILEILELL9 - 4339 - 433
12112161LYSLYSII9 - 4349 - 434
12212261LYSLYSJJ9 - 4349 - 434
12312362ARGARGII9 - 4329 - 432
12412462ARGARGKK9 - 4329 - 432
12512563ILEILEII9 - 4339 - 433
12612663ILEILELL9 - 4339 - 433
12712764ARGARGJJ9 - 4329 - 432
12812864ARGARGKK9 - 4329 - 432
12912965ILEILEJJ9 - 4339 - 433
13013065ILEILELL9 - 4339 - 433
13113166ARGARGKK9 - 4329 - 432
13213266ARGARGLL9 - 4329 - 432

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28
15Local NCS retraints between domains: 29 30
16Local NCS retraints between domains: 31 32
17Local NCS retraints between domains: 33 34
18Local NCS retraints between domains: 35 36
19Local NCS retraints between domains: 37 38
20Local NCS retraints between domains: 39 40
21Local NCS retraints between domains: 41 42
22Local NCS retraints between domains: 43 44
23Local NCS retraints between domains: 45 46
24Local NCS retraints between domains: 47 48
25Local NCS retraints between domains: 49 50
26Local NCS retraints between domains: 51 52
27Local NCS retraints between domains: 53 54
28Local NCS retraints between domains: 55 56
29Local NCS retraints between domains: 57 58
30Local NCS retraints between domains: 59 60
31Local NCS retraints between domains: 61 62
32Local NCS retraints between domains: 63 64
33Local NCS retraints between domains: 65 66
34Local NCS retraints between domains: 67 68
35Local NCS retraints between domains: 69 70
36Local NCS retraints between domains: 71 72
37Local NCS retraints between domains: 73 74
38Local NCS retraints between domains: 75 76
39Local NCS retraints between domains: 77 78
40Local NCS retraints between domains: 79 80
41Local NCS retraints between domains: 81 82
42Local NCS retraints between domains: 83 84
43Local NCS retraints between domains: 85 86
44Local NCS retraints between domains: 87 88
45Local NCS retraints between domains: 89 90
46Local NCS retraints between domains: 91 92
47Local NCS retraints between domains: 93 94
48Local NCS retraints between domains: 95 96
49Local NCS retraints between domains: 97 98
50Local NCS retraints between domains: 99 100
51Local NCS retraints between domains: 101 102
52Local NCS retraints between domains: 103 104
53Local NCS retraints between domains: 105 106
54Local NCS retraints between domains: 107 108
55Local NCS retraints between domains: 109 110
56Local NCS retraints between domains: 111 112
57Local NCS retraints between domains: 113 114
58Local NCS retraints between domains: 115 116
59Local NCS retraints between domains: 117 118
60Local NCS retraints between domains: 119 120
61Local NCS retraints between domains: 121 122
62Local NCS retraints between domains: 123 124
63Local NCS retraints between domains: 125 126
64Local NCS retraints between domains: 127 128
65Local NCS retraints between domains: 129 130
66Local NCS retraints between domains: 131 132

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Components

#1: Protein
Oxalate--CoA ligase / Acyl-activating enzyme 3 / Oxalyl-CoA synthetase / Peroxisomal-coenzyme A synthetase


Mass: 60562.410 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PCS60, AAE3, FAT2, YBR222C, YBR1512 / Production host: Escherichia coli (E. coli) / References: UniProt: P38137, oxalate-CoA ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M LiCl, 0.1M Hepes pH 8.0, 10-16% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.87→29.985 Å / Num. obs: 163072 / % possible obs: 99.2 % / Redundancy: 1.9 % / CC1/2: 0.99 / Net I/σ(I): 8.6
Reflection shellResolution: 2.87→2.97 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 8029 / CC1/2: 0.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.87→29.985 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.912 / SU B: 47.526 / SU ML: 0.387 / Cross valid method: FREE R-VALUE / ESU R Free: 0.384 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2497 8186 5.021 %
Rwork0.2274 154841 -
all0.229 --
obs-163027 99.003 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 80.108 Å2
Baniso -1Baniso -2Baniso -3
1-1.818 Å20 Å2-1.017 Å2
2---1.195 Å20 Å2
3----0.483 Å2
Refinement stepCycle: LAST / Resolution: 2.87→29.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42466 0 0 317 42783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01243562
X-RAY DIFFRACTIONr_angle_refined_deg1.751.64159231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.65155382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45422.5522147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.637157143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.11515222
X-RAY DIFFRACTIONr_chiral_restr0.1590.25751
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0233213
X-RAY DIFFRACTIONr_nbd_refined0.1720.218163
X-RAY DIFFRACTIONr_nbtor_refined0.290.229556
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.21171
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.350.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2680.24
X-RAY DIFFRACTIONr_mcbond_it1.461.79421567
X-RAY DIFFRACTIONr_mcangle_it2.5222.68626936
X-RAY DIFFRACTIONr_scbond_it1.3031.83121995
X-RAY DIFFRACTIONr_scangle_it2.2162.72332295
X-RAY DIFFRACTIONr_lrange_it5.43923.48662083
X-RAY DIFFRACTIONr_ncsr_local_group_10.0460.0514347
X-RAY DIFFRACTIONr_ncsr_local_group_20.0450.0514385
X-RAY DIFFRACTIONr_ncsr_local_group_30.0440.0516711
X-RAY DIFFRACTIONr_ncsr_local_group_40.0380.0514307
X-RAY DIFFRACTIONr_ncsr_local_group_50.0390.0514382
X-RAY DIFFRACTIONr_ncsr_local_group_60.0340.0514222
X-RAY DIFFRACTIONr_ncsr_local_group_70.0450.0514281
X-RAY DIFFRACTIONr_ncsr_local_group_80.0490.0516838
X-RAY DIFFRACTIONr_ncsr_local_group_90.040.0514316
X-RAY DIFFRACTIONr_ncsr_local_group_100.040.0514246
X-RAY DIFFRACTIONr_ncsr_local_group_110.040.0514319
X-RAY DIFFRACTIONr_ncsr_local_group_120.0460.0514406
X-RAY DIFFRACTIONr_ncsr_local_group_130.0420.0514385
X-RAY DIFFRACTIONr_ncsr_local_group_140.0320.0514403
X-RAY DIFFRACTIONr_ncsr_local_group_150.0390.0514395
X-RAY DIFFRACTIONr_ncsr_local_group_160.0440.0514219
X-RAY DIFFRACTIONr_ncsr_local_group_170.040.0514372
X-RAY DIFFRACTIONr_ncsr_local_group_180.0460.0514375
X-RAY DIFFRACTIONr_ncsr_local_group_190.0390.0514382
X-RAY DIFFRACTIONr_ncsr_local_group_200.0430.0514317
X-RAY DIFFRACTIONr_ncsr_local_group_210.0440.0514342
X-RAY DIFFRACTIONr_ncsr_local_group_220.0460.0514433
X-RAY DIFFRACTIONr_ncsr_local_group_230.0390.0514346
X-RAY DIFFRACTIONr_ncsr_local_group_240.0440.0514411
X-RAY DIFFRACTIONr_ncsr_local_group_250.040.0514229
X-RAY DIFFRACTIONr_ncsr_local_group_260.0460.0514327
X-RAY DIFFRACTIONr_ncsr_local_group_270.0490.0514379
X-RAY DIFFRACTIONr_ncsr_local_group_280.0410.0514366
X-RAY DIFFRACTIONr_ncsr_local_group_290.0430.0514280
X-RAY DIFFRACTIONr_ncsr_local_group_300.040.0514343
X-RAY DIFFRACTIONr_ncsr_local_group_310.0320.0514354
X-RAY DIFFRACTIONr_ncsr_local_group_320.0370.0514393
X-RAY DIFFRACTIONr_ncsr_local_group_330.0290.0514231
X-RAY DIFFRACTIONr_ncsr_local_group_340.0370.0514356
X-RAY DIFFRACTIONr_ncsr_local_group_350.0460.0516509
X-RAY DIFFRACTIONr_ncsr_local_group_360.0380.0514346
X-RAY DIFFRACTIONr_ncsr_local_group_370.0380.0514274
X-RAY DIFFRACTIONr_ncsr_local_group_380.0380.0514336
X-RAY DIFFRACTIONr_ncsr_local_group_390.030.0514341
X-RAY DIFFRACTIONr_ncsr_local_group_400.0340.0514222
X-RAY DIFFRACTIONr_ncsr_local_group_410.0340.0514373
X-RAY DIFFRACTIONr_ncsr_local_group_420.0340.0514345
X-RAY DIFFRACTIONr_ncsr_local_group_430.0310.0514373
X-RAY DIFFRACTIONr_ncsr_local_group_440.0330.0514318
X-RAY DIFFRACTIONr_ncsr_local_group_450.0350.0514379
X-RAY DIFFRACTIONr_ncsr_local_group_460.030.0514228
X-RAY DIFFRACTIONr_ncsr_local_group_470.0320.0514353
X-RAY DIFFRACTIONr_ncsr_local_group_480.0410.0514364
X-RAY DIFFRACTIONr_ncsr_local_group_490.0290.0514369
X-RAY DIFFRACTIONr_ncsr_local_group_500.0360.0514290
X-RAY DIFFRACTIONr_ncsr_local_group_510.0310.0514368
X-RAY DIFFRACTIONr_ncsr_local_group_520.0370.0514206
X-RAY DIFFRACTIONr_ncsr_local_group_530.0330.0514216
X-RAY DIFFRACTIONr_ncsr_local_group_540.0350.0514225
X-RAY DIFFRACTIONr_ncsr_local_group_550.0370.0514235
X-RAY DIFFRACTIONr_ncsr_local_group_560.0330.0514249
X-RAY DIFFRACTIONr_ncsr_local_group_570.0380.0514330
X-RAY DIFFRACTIONr_ncsr_local_group_580.0370.0514385
X-RAY DIFFRACTIONr_ncsr_local_group_590.0380.0514296
X-RAY DIFFRACTIONr_ncsr_local_group_600.0340.0514361
X-RAY DIFFRACTIONr_ncsr_local_group_610.0360.0514344
X-RAY DIFFRACTIONr_ncsr_local_group_620.0380.0514291
X-RAY DIFFRACTIONr_ncsr_local_group_630.040.0514315
X-RAY DIFFRACTIONr_ncsr_local_group_640.0370.0514289
X-RAY DIFFRACTIONr_ncsr_local_group_650.0350.0514344
X-RAY DIFFRACTIONr_ncsr_local_group_660.0370.0514309
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.045970.0501
12BX-RAY DIFFRACTIONLocal ncs0.045970.0501
23AX-RAY DIFFRACTIONLocal ncs0.045150.0501
24CX-RAY DIFFRACTIONLocal ncs0.045150.0501
35AX-RAY DIFFRACTIONLocal ncs0.043930.05009
36DX-RAY DIFFRACTIONLocal ncs0.043930.05009
47AX-RAY DIFFRACTIONLocal ncs0.037790.0501
48EX-RAY DIFFRACTIONLocal ncs0.037790.0501
59AX-RAY DIFFRACTIONLocal ncs0.038940.0501
510FX-RAY DIFFRACTIONLocal ncs0.038940.0501
611AX-RAY DIFFRACTIONLocal ncs0.03420.0501
612GX-RAY DIFFRACTIONLocal ncs0.03420.0501
713AX-RAY DIFFRACTIONLocal ncs0.04480.0501
714HX-RAY DIFFRACTIONLocal ncs0.04480.0501
815AX-RAY DIFFRACTIONLocal ncs0.049490.05009
816IX-RAY DIFFRACTIONLocal ncs0.049490.05009
917AX-RAY DIFFRACTIONLocal ncs0.039890.0501
918JX-RAY DIFFRACTIONLocal ncs0.039890.0501
1019AX-RAY DIFFRACTIONLocal ncs0.039930.0501
1020KX-RAY DIFFRACTIONLocal ncs0.039930.0501
1121AX-RAY DIFFRACTIONLocal ncs0.039530.0501
1122LX-RAY DIFFRACTIONLocal ncs0.039530.0501
1223BX-RAY DIFFRACTIONLocal ncs0.045580.0501
1224CX-RAY DIFFRACTIONLocal ncs0.045580.0501
1325BX-RAY DIFFRACTIONLocal ncs0.041880.0501
1326DX-RAY DIFFRACTIONLocal ncs0.041880.0501
1427BX-RAY DIFFRACTIONLocal ncs0.031650.0501
1428EX-RAY DIFFRACTIONLocal ncs0.031650.0501
1529BX-RAY DIFFRACTIONLocal ncs0.038890.0501
1530FX-RAY DIFFRACTIONLocal ncs0.038890.0501
1631BX-RAY DIFFRACTIONLocal ncs0.043610.0501
1632GX-RAY DIFFRACTIONLocal ncs0.043610.0501
1733BX-RAY DIFFRACTIONLocal ncs0.040350.0501
1734HX-RAY DIFFRACTIONLocal ncs0.040350.0501
1835BX-RAY DIFFRACTIONLocal ncs0.046230.0501
1836IX-RAY DIFFRACTIONLocal ncs0.046230.0501
1937BX-RAY DIFFRACTIONLocal ncs0.038780.0501
1938JX-RAY DIFFRACTIONLocal ncs0.038780.0501
2039BX-RAY DIFFRACTIONLocal ncs0.043470.0501
2040KX-RAY DIFFRACTIONLocal ncs0.043470.0501
2141BX-RAY DIFFRACTIONLocal ncs0.043570.0501
2142LX-RAY DIFFRACTIONLocal ncs0.043570.0501
2243CX-RAY DIFFRACTIONLocal ncs0.045570.0501
2244DX-RAY DIFFRACTIONLocal ncs0.045570.0501
2345CX-RAY DIFFRACTIONLocal ncs0.038860.0501
2346EX-RAY DIFFRACTIONLocal ncs0.038860.0501
2447CX-RAY DIFFRACTIONLocal ncs0.043540.0501
2448FX-RAY DIFFRACTIONLocal ncs0.043540.0501
2549CX-RAY DIFFRACTIONLocal ncs0.039540.0501
2550GX-RAY DIFFRACTIONLocal ncs0.039540.0501
2651CX-RAY DIFFRACTIONLocal ncs0.045710.0501
2652HX-RAY DIFFRACTIONLocal ncs0.045710.0501
2753CX-RAY DIFFRACTIONLocal ncs0.049130.0501
2754IX-RAY DIFFRACTIONLocal ncs0.049130.0501
2855CX-RAY DIFFRACTIONLocal ncs0.041070.0501
2856JX-RAY DIFFRACTIONLocal ncs0.041070.0501
2957CX-RAY DIFFRACTIONLocal ncs0.042510.0501
2958KX-RAY DIFFRACTIONLocal ncs0.042510.0501
3059CX-RAY DIFFRACTIONLocal ncs0.040440.0501
3060LX-RAY DIFFRACTIONLocal ncs0.040440.0501
3161DX-RAY DIFFRACTIONLocal ncs0.031920.0501
3162EX-RAY DIFFRACTIONLocal ncs0.031920.0501
3263DX-RAY DIFFRACTIONLocal ncs0.036680.0501
3264FX-RAY DIFFRACTIONLocal ncs0.036680.0501
3365DX-RAY DIFFRACTIONLocal ncs0.028960.0501
3366GX-RAY DIFFRACTIONLocal ncs0.028960.0501
3467DX-RAY DIFFRACTIONLocal ncs0.037260.0501
3468HX-RAY DIFFRACTIONLocal ncs0.037260.0501
3569DX-RAY DIFFRACTIONLocal ncs0.045520.0501
3570IX-RAY DIFFRACTIONLocal ncs0.045520.0501
3671DX-RAY DIFFRACTIONLocal ncs0.037670.0501
3672JX-RAY DIFFRACTIONLocal ncs0.037670.0501
3773DX-RAY DIFFRACTIONLocal ncs0.037530.0501
3774KX-RAY DIFFRACTIONLocal ncs0.037530.0501
3875DX-RAY DIFFRACTIONLocal ncs0.037630.0501
3876LX-RAY DIFFRACTIONLocal ncs0.037630.0501
3977EX-RAY DIFFRACTIONLocal ncs0.030050.0501
3978FX-RAY DIFFRACTIONLocal ncs0.030050.0501
4079EX-RAY DIFFRACTIONLocal ncs0.033680.0501
4080GX-RAY DIFFRACTIONLocal ncs0.033680.0501
4181EX-RAY DIFFRACTIONLocal ncs0.034130.0501
4182HX-RAY DIFFRACTIONLocal ncs0.034130.0501
4283EX-RAY DIFFRACTIONLocal ncs0.033830.0501
4284IX-RAY DIFFRACTIONLocal ncs0.033830.0501
4385EX-RAY DIFFRACTIONLocal ncs0.030760.0501
4386JX-RAY DIFFRACTIONLocal ncs0.030760.0501
4487EX-RAY DIFFRACTIONLocal ncs0.032590.0501
4488KX-RAY DIFFRACTIONLocal ncs0.032590.0501
4589EX-RAY DIFFRACTIONLocal ncs0.035420.0501
4590LX-RAY DIFFRACTIONLocal ncs0.035420.0501
4691FX-RAY DIFFRACTIONLocal ncs0.030430.0501
4692GX-RAY DIFFRACTIONLocal ncs0.030430.0501
4793FX-RAY DIFFRACTIONLocal ncs0.032120.0501
4794HX-RAY DIFFRACTIONLocal ncs0.032120.0501
4895FX-RAY DIFFRACTIONLocal ncs0.040740.0501
4896IX-RAY DIFFRACTIONLocal ncs0.040740.0501
4997FX-RAY DIFFRACTIONLocal ncs0.029260.0501
4998JX-RAY DIFFRACTIONLocal ncs0.029260.0501
5099FX-RAY DIFFRACTIONLocal ncs0.036060.0501
50100KX-RAY DIFFRACTIONLocal ncs0.036060.0501
51101FX-RAY DIFFRACTIONLocal ncs0.031480.0501
51102LX-RAY DIFFRACTIONLocal ncs0.031480.0501
52103GX-RAY DIFFRACTIONLocal ncs0.037260.0501
52104HX-RAY DIFFRACTIONLocal ncs0.037260.0501
53105GX-RAY DIFFRACTIONLocal ncs0.033060.0501
53106IX-RAY DIFFRACTIONLocal ncs0.033060.0501
54107GX-RAY DIFFRACTIONLocal ncs0.034730.0501
54108JX-RAY DIFFRACTIONLocal ncs0.034730.0501
55109GX-RAY DIFFRACTIONLocal ncs0.036560.0501
55110KX-RAY DIFFRACTIONLocal ncs0.036560.0501
56111GX-RAY DIFFRACTIONLocal ncs0.033450.0501
56112LX-RAY DIFFRACTIONLocal ncs0.033450.0501
57113HX-RAY DIFFRACTIONLocal ncs0.03850.0501
57114IX-RAY DIFFRACTIONLocal ncs0.03850.0501
58115HX-RAY DIFFRACTIONLocal ncs0.037270.0501
58116JX-RAY DIFFRACTIONLocal ncs0.037270.0501
59117HX-RAY DIFFRACTIONLocal ncs0.037990.0501
59118KX-RAY DIFFRACTIONLocal ncs0.037990.0501
60119HX-RAY DIFFRACTIONLocal ncs0.034360.0501
60120LX-RAY DIFFRACTIONLocal ncs0.034360.0501
61121IX-RAY DIFFRACTIONLocal ncs0.036080.0501
61122JX-RAY DIFFRACTIONLocal ncs0.036080.0501
62123IX-RAY DIFFRACTIONLocal ncs0.037810.0501
62124KX-RAY DIFFRACTIONLocal ncs0.037810.0501
63125IX-RAY DIFFRACTIONLocal ncs0.039630.0501
63126LX-RAY DIFFRACTIONLocal ncs0.039630.0501
64127JX-RAY DIFFRACTIONLocal ncs0.037120.0501
64128KX-RAY DIFFRACTIONLocal ncs0.037120.0501
65129JX-RAY DIFFRACTIONLocal ncs0.0350.0501
65130LX-RAY DIFFRACTIONLocal ncs0.0350.0501
66131KX-RAY DIFFRACTIONLocal ncs0.036710.0501
66132LX-RAY DIFFRACTIONLocal ncs0.036710.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-2.9450.3616290.36211414X-RAY DIFFRACTION99.6112
2.945-3.0250.3596110.34411122X-RAY DIFFRACTION99.5503
3.025-3.1130.345590.32110826X-RAY DIFFRACTION98.9312
3.113-3.2090.3415490.3110589X-RAY DIFFRACTION99.7046
3.209-3.3140.315420.29310144X-RAY DIFFRACTION99.34
3.314-3.430.2875220.2729880X-RAY DIFFRACTION99.1328
3.43-3.560.2884900.2659381X-RAY DIFFRACTION98.1701
3.56-3.7050.2735220.2489060X-RAY DIFFRACTION98.4587
3.705-3.870.2464600.2278858X-RAY DIFFRACTION99.3284
3.87-4.0590.2494720.2228186X-RAY DIFFRACTION97.0301
4.059-4.2780.2264360.1948004X-RAY DIFFRACTION99.54
4.278-4.5380.2053640.1897655X-RAY DIFFRACTION99.1714
4.538-4.8510.1963510.1777170X-RAY DIFFRACTION99.5763
4.851-5.2390.2243310.1826738X-RAY DIFFRACTION99.7742
5.239-5.7390.23160.1846191X-RAY DIFFRACTION99.5411
5.739-6.4170.2472920.2025575X-RAY DIFFRACTION99.407
6.417-7.4090.2092690.1964903X-RAY DIFFRACTION99.3469
7.409-9.0730.1932210.1814199X-RAY DIFFRACTION98.8814
9.073-12.8270.1711630.1673249X-RAY DIFFRACTION98.7554
12.827-29.9850.265870.2541697X-RAY DIFFRACTION89.2446
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.3552-0.33170.41750.5766-0.02751.06290.0723-0.012-0.2659-0.0577-0.12320.42680.1783-0.08540.0510.9374-0.0491-0.13740.4432-0.09810.8161-122.8916-21.4797141.5323
20.6631-0.19220.16960.39140.16280.70810.0259-0.01740.0465-0.0678-0.10960.2734-0.1052-0.05460.08370.9170.0795-0.10760.4256-0.04850.6868-124.707721.6779144.3288
30.64050.0631-0.05560.9064-0.14520.836-0.0541-0.0177-0.07390.19090.0346-0.0950.07970.13850.01950.90970.0482-0.15830.48850.00240.5005-76.6064-13.624157.989
41.25910.3522-0.01290.3245-0.15631.2210.0364-0.1760.13980.08370.00940.0958-0.32370.2165-0.04580.9947-0.0899-0.1250.4445-0.0560.485-76.990528.8298154.2765
50.61060.15140.19160.16280.24440.9379-0.04640.1482-0.2171-0.19050.16830.06650.03660.3874-0.12181.1692-0.0647-0.09620.5908-0.16820.4527-74.262-18.6483107.5862
60.18740.09350.21480.18960.27850.9172-0.3625-0.03290.0028-0.47780.19730.1394-0.48810.20450.16521.5652-0.2935-0.39460.42480.07810.2798-88.60818.3722101.2227
70.95080.05210.96170.1011-0.07011.4941-0.4233-0.42340.08660.27430.0818-0.1487-0.6141-0.61480.34161.43240.1206-0.4640.8012-0.22060.2574-35.10228.638777.9818
80.91610.16920.00140.20330.00760.6961-0.0603-0.0959-0.08590.3845-0.0055-0.07480.4943-0.2260.06581.2485-0.185-0.10710.64130.15560.3052-37.949-30.740570.4753
91.3887-0.15680.36980.50150.07010.6304-0.14310.20560.2745-0.0833-0.005-0.0475-0.2735-0.21410.14810.84510.0729-0.09720.72330.01030.5834-47.867916.732223.947
100.43270.08080.26830.44740.21491.11280.26440.1607-0.1191-0.0363-0.0892-0.10220.2601-0.0473-0.17520.865-0.0197-0.0620.6422-0.10860.603-35.9242-24.079119.9775
110.84480.23970.40610.22930.15890.6072-0.11650.19730.0480.1339-0.2356-0.1625-0.23840.03970.35210.757-0.25-0.20160.64620.31780.7498-0.363123.012535.0873
120.89740.26640.61350.26990.1470.64980.220.2062-0.45330.1996-0.1909-0.50190.10210.0903-0.02910.51440.0401-0.31540.56020.28841.17169.0042-15.274642.747
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA9 - 533
2X-RAY DIFFRACTION2ALLB9 - 436
3X-RAY DIFFRACTION3ALLC9 - 438
4X-RAY DIFFRACTION4ALLD9 - 519
5X-RAY DIFFRACTION5ALLE9 - 434
6X-RAY DIFFRACTION6ALLF9 - 437
7X-RAY DIFFRACTION7ALLG9 - 431
8X-RAY DIFFRACTION8ALLH9 - 435
9X-RAY DIFFRACTION9ALLI9 - 532
10X-RAY DIFFRACTION10ALLJ9 - 435
11X-RAY DIFFRACTION11ALLK9 - 433
12X-RAY DIFFRACTION12ALLL9 - 434

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