[English] 日本語
Yorodumi
- PDB-25hn: Cryo-EM structure of native Rubisco from Nitrosospira multiformis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 25hn
TitleCryo-EM structure of native Rubisco from Nitrosospira multiformis
Components
  • Ribulose bisphosphate carboxylase large chain
  • Ribulose bisphosphate carboxylase small subunit
KeywordsLYASE / rubisco / carbon fixation / nitrifying bacterium / autotrophy / cryo-EM
Function / homology
Function and homology information


ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain ...Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit
Similarity search - Component
Biological speciesNitrosospira multiformis ATCC 25196 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.26 Å
AuthorsTanaka, Y. / Nishigaya, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem Biophys Res Commun / Year: 2026
Title: Cryo-EM structure of RubisCO from Nitrosospira multiformis.
Authors: Yoshiki Tanaka / Yuki Nishigaya /
Abstract: Nitrosospira multiformis is a soil ammonia-oxidizing bacterium (AOB) that fixes CO via RubisCO using energy derived from ammonia oxidation. Despite its ecological and agricultural relevance, the ...Nitrosospira multiformis is a soil ammonia-oxidizing bacterium (AOB) that fixes CO via RubisCO using energy derived from ammonia oxidation. Despite its ecological and agricultural relevance, the structure of N. multiformis RubisCO (NmRubisCO) remained unknown. Here, we report the cryo-EM structure of NmRubisCO at 2.26 Å resolution, determined through single-particle analysis of protein copurified with the membrane fraction following cell lysis and ultracentrifugation without column chromatography. Analysis revealed an LS hexadecameric Form IC (red-like) RubisCO with a six-residue insertion in the βB-βC loop (BC loop) of the large-subunit N-terminal domain that forms a solvent-exposed, well-ordered protrusion. The active site lacks carbamylation at K206 and Mg binding, representing an inactive state. A putative metal ion coordinated by H296, H298, and H331, tentatively assigned as Zn based on coordination geometry and distances, was identified near the catalytic center; this His-coordinated metal site has not been described in other RubisCO structures. Loop 6 adopts a closed-like conformation in the absence of substrate, a configuration consistent with a potential requirement for activase-mediated remodeling. The C-terminal extension of the small subunit forms interdimer β-sheet interactions that stabilize the holoenzyme. These structural features provide a framework for understanding Form IC RubisCO in carboxysome-less soil AOB.
History
DepositionApr 3, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase large chain
C: Ribulose bisphosphate carboxylase large chain
E: Ribulose bisphosphate carboxylase large chain
F: Ribulose bisphosphate carboxylase large chain
I: Ribulose bisphosphate carboxylase large chain
J: Ribulose bisphosphate carboxylase large chain
M: Ribulose bisphosphate carboxylase large chain
N: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase small subunit
D: Ribulose bisphosphate carboxylase small subunit
G: Ribulose bisphosphate carboxylase small subunit
H: Ribulose bisphosphate carboxylase small subunit
K: Ribulose bisphosphate carboxylase small subunit
L: Ribulose bisphosphate carboxylase small subunit
O: Ribulose bisphosphate carboxylase small subunit
P: Ribulose bisphosphate carboxylase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)570,01024
Polymers569,48616
Non-polymers5238
Water7,800433
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21C
32A
42E
53A
63F
74A
84I
95A
105J
116A
126M
137A
147N
158C
168E
179C
189F
1910C
2010I
2111C
2211J
2312C
2412M
2513C
2613N
2714E
2814F
2915E
3015I
3116E
3216J
3317E
3417M
3518E
3618N
3719F
3819I
3920F
4020J
4121F
4221M
4322F
4422N
4523I
4623J
4724I
4824M
4925I
5025N
5126J
5226M
5327J
5427N
5528M
5628N
5729B
5829D
5930B
6030G
6131B
6231H
6332B
6432K
6533B
6633L
6734B
6834O
6935B
7035P
7136D
7236G
7337D
7437H
7538D
7638K
7739D
7839L
7940D
8040O
8141D
8241P
8342G
8442H
8543G
8643K
8744G
8844L
8945G
9045O
9146G
9246P
9347H
9447K
9548H
9648L
9749H
9849O
9950H
10050P
10151K
10251L
10352K
10452O
10553K
10653P
10754L
10854O
10955L
11055P
11156O
11256P

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ILEILEILEILEAA16 - 46916 - 469
211ILEILEILEILECB16 - 46916 - 469
322ILEILEILEILEAA16 - 46916 - 469
422ILEILEILEILEEC16 - 46916 - 469
533ILEILEILEILEAA16 - 46916 - 469
633ILEILEILEILEFD16 - 46916 - 469
744ILEILEILEILEAA16 - 46916 - 469
844ILEILEILEILEIE16 - 46916 - 469
955ILEILEILEILEAA16 - 46916 - 469
1055ILEILEILEILEJF16 - 46916 - 469
1166ILEILEILEILEAA16 - 46916 - 469
1266ILEILEILEILEMG16 - 46916 - 469
1377ILEILEILEILEAA16 - 46916 - 469
1477ILEILEILEILENH16 - 46916 - 469
1588ILEILEILEILECB16 - 46916 - 469
1688ILEILEILEILEEC16 - 46916 - 469
1799ILEILEILEILECB16 - 46916 - 469
1899ILEILEILEILEFD16 - 46916 - 469
191010ILEILEILEILECB16 - 46916 - 469
201010ILEILEILEILEIE16 - 46916 - 469
211111ILEILEILEILECB16 - 46916 - 469
221111ILEILEILEILEJF16 - 46916 - 469
231212ILEILEILEILECB16 - 46916 - 469
241212ILEILEILEILEMG16 - 46916 - 469
251313ILEILEILEILECB16 - 46916 - 469
261313ILEILEILEILENH16 - 46916 - 469
271414ILEILEILEILEEC16 - 46916 - 469
281414ILEILEILEILEFD16 - 46916 - 469
291515ILEILEILEILEEC16 - 46916 - 469
301515ILEILEILEILEIE16 - 46916 - 469
311616ILEILEILEILEEC16 - 46916 - 469
321616ILEILEILEILEJF16 - 46916 - 469
331717ILEILEILEILEEC16 - 46916 - 469
341717ILEILEILEILEMG16 - 46916 - 469
351818ILEILEILEILEEC16 - 46916 - 469
361818ILEILEILEILENH16 - 46916 - 469
371919ILEILEILEILEFD16 - 46916 - 469
381919ILEILEILEILEIE16 - 46916 - 469
392020ILEILEILEILEFD16 - 46916 - 469
402020ILEILEILEILEJF16 - 46916 - 469
412121ILEILEILEILEFD16 - 46916 - 469
422121ILEILEILEILEMG16 - 46916 - 469
432222ILEILEILEILEFD16 - 46916 - 469
442222ILEILEILEILENH16 - 46916 - 469
452323ILEILEILEILEIE16 - 46916 - 469
462323ILEILEILEILEJF16 - 46916 - 469
472424ILEILEILEILEIE16 - 46916 - 469
482424ILEILEILEILEMG16 - 46916 - 469
492525ILEILEILEILEIE16 - 46916 - 469
502525ILEILEILEILENH16 - 46916 - 469
512626ILEILEILEILEJF16 - 46916 - 469
522626ILEILEILEILEMG16 - 46916 - 469
532727ILEILEILEILEJF16 - 46916 - 469
542727ILEILEILEILENH16 - 46916 - 469
552828ILEILEILEILEMG16 - 46916 - 469
562828ILEILEILEILENH16 - 46916 - 469
572929METMETTYRTYRBI1 - 1441 - 144
582929METMETTYRTYRDJ1 - 1441 - 144
593030METMETTYRTYRBI1 - 1441 - 144
603030METMETTYRTYRGK1 - 1441 - 144
613131METMETTYRTYRBI1 - 1441 - 144
623131METMETTYRTYRHL1 - 1441 - 144
633232METMETTYRTYRBI1 - 1441 - 144
643232METMETTYRTYRKM1 - 1441 - 144
653333METMETTYRTYRBI1 - 1441 - 144
663333METMETTYRTYRLN1 - 1441 - 144
673434METMETTYRTYRBI1 - 1441 - 144
683434METMETTYRTYROO1 - 1441 - 144
693535METMETTYRTYRBI1 - 1441 - 144
703535METMETTYRTYRPP1 - 1441 - 144
713636METMETTYRTYRDJ1 - 1441 - 144
723636METMETTYRTYRGK1 - 1441 - 144
733737METMETTYRTYRDJ1 - 1441 - 144
743737METMETTYRTYRHL1 - 1441 - 144
753838METMETTYRTYRDJ1 - 1441 - 144
763838METMETTYRTYRKM1 - 1441 - 144
773939METMETTYRTYRDJ1 - 1441 - 144
783939METMETTYRTYRLN1 - 1441 - 144
794040METMETTYRTYRDJ1 - 1441 - 144
804040METMETTYRTYROO1 - 1441 - 144
814141METMETTYRTYRDJ1 - 1441 - 144
824141METMETTYRTYRPP1 - 1441 - 144
834242METMETTYRTYRGK1 - 1441 - 144
844242METMETTYRTYRHL1 - 1441 - 144
854343METMETTYRTYRGK1 - 1441 - 144
864343METMETTYRTYRKM1 - 1441 - 144
874444METMETTYRTYRGK1 - 1441 - 144
884444METMETTYRTYRLN1 - 1441 - 144
894545METMETTYRTYRGK1 - 1441 - 144
904545METMETTYRTYROO1 - 1441 - 144
914646METMETTYRTYRGK1 - 1441 - 144
924646METMETTYRTYRPP1 - 1441 - 144
934747METMETTYRTYRHL1 - 1441 - 144
944747METMETTYRTYRKM1 - 1441 - 144
954848METMETTYRTYRHL1 - 1441 - 144
964848METMETTYRTYRLN1 - 1441 - 144
974949METMETTYRTYRHL1 - 1441 - 144
984949METMETTYRTYROO1 - 1441 - 144
995050METMETTYRTYRHL1 - 1441 - 144
1005050METMETTYRTYRPP1 - 1441 - 144
1015151METMETTYRTYRKM1 - 1441 - 144
1025151METMETTYRTYRLN1 - 1441 - 144
1035252METMETTYRTYRKM1 - 1441 - 144
1045252METMETTYRTYROO1 - 1441 - 144
1055353METMETTYRTYRKM1 - 1441 - 144
1065353METMETTYRTYRPP1 - 1441 - 144
1075454METMETTYRTYRLN1 - 1441 - 144
1085454METMETTYRTYROO1 - 1441 - 144
1095555METMETTYRTYRLN1 - 1441 - 144
1105555METMETTYRTYRPP1 - 1441 - 144
1115656METMETTYRTYROO1 - 1441 - 144
1125656METMETTYRTYRPP1 - 1441 - 144

NCS ensembles :
IDDetails (eV)
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

-
Components

#1: Protein
Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit


Mass: 54379.926 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Nitrosospira multiformis ATCC 25196 (bacteria)
References: UniProt: Q2YB78, ribulose-bisphosphate carboxylase
#2: Protein
Ribulose bisphosphate carboxylase small subunit / RuBisCO small subunit


Mass: 16805.855 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Nitrosospira multiformis ATCC 25196 (bacteria)
References: UniProt: Q2YB79
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Ribulose bisphosphate carboxylase / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 0.56 MDa / Experimental value: NO
Source (natural)Organism: Nitrosospira multiformis ATCC 25196 (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1250 mMsodium chlorideNaCl1
225 mMPIPESC8H18N2O6S21
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Total protein concentration of the membrane suspension
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 57000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 10080
EM imaging opticsEnergyfilter name: In-column Omega Filter / Phase plate: VOLTA PHASE PLATE

-
Processing

EM software
IDNameVersionCategory
1RELION5.0.1particle selection
2SerialEMimage acquisition
4CTFFIND4.1.14CTF correction
7Coot0.9.8model fitting
9RELION5.0.1initial Euler assignment
10RELION5.0.1final Euler assignment
11RELION5.0.1classification
12RELION5.0.13D reconstruction
13Servalcat0.4.131model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1577431
Details: Perform 2D sorting on the particles collected via LoG picking, train Topaz on the useful ones, and then perform Topaz picking
SymmetryPoint symmetry: D4 (2x4 fold dihedral)
3D reconstructionResolution: 2.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64288 / Algorithm: BACK PROJECTION / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 4F0H

4f0h


Accession code: 4F0H / Source name: PDB / Type: experimental model
RefinementResolution: 2.26→138.787 Å / Cor.coef. Fo:Fc: 0.936 / WRfactor Rwork: 0.285 / SU B: 3.937 / SU ML: 0.089 / Average fsc free: 0 / Average fsc overall: 0.8707 / Average fsc work: 0.8707 / ESU R: 0.221
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.285 478868 -
all0.285 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 105.45 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0120.01238912
ELECTRON MICROSCOPYr_bond_other_d00.01636464
ELECTRON MICROSCOPYr_angle_refined_deg1.9191.82352712
ELECTRON MICROSCOPYr_angle_other_deg0.6251.76583880
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.08854784
ELECTRON MICROSCOPYr_dihedral_angle_2_deg6.9415272
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.32106560
ELECTRON MICROSCOPYr_dihedral_angle_6_deg15.087101840
ELECTRON MICROSCOPYr_chiral_restr0.0970.25584
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.0246496
ELECTRON MICROSCOPYr_gen_planes_other0.0010.029264
ELECTRON MICROSCOPYr_nbd_refined0.220.28209
ELECTRON MICROSCOPYr_symmetry_nbd_other0.2120.235423
ELECTRON MICROSCOPYr_nbtor_refined0.1890.219458
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0830.221471
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.2310.2838
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_other0.0230.21
ELECTRON MICROSCOPYr_mcbond_it11.3319.92919160
ELECTRON MICROSCOPYr_mcbond_other11.339.92919160
ELECTRON MICROSCOPYr_mcangle_it15.88217.85723936
ELECTRON MICROSCOPYr_mcangle_other15.88317.85823937
ELECTRON MICROSCOPYr_scbond_it12.65911.05819752
ELECTRON MICROSCOPYr_scbond_other12.65911.05819752
ELECTRON MICROSCOPYr_scangle_it18.52919.77328776
ELECTRON MICROSCOPYr_scangle_other18.52919.77328777
ELECTRON MICROSCOPYr_lrange_it24.65494.42643347
ELECTRON MICROSCOPYr_lrange_other24.65494.42743348
ELECTRON MICROSCOPYr_ncsr_local_group_10.0810.0514632
ELECTRON MICROSCOPYr_ncsr_local_group_20.0750.0514666
ELECTRON MICROSCOPYr_ncsr_local_group_30.0740.0514721
ELECTRON MICROSCOPYr_ncsr_local_group_40.0740.0514625
ELECTRON MICROSCOPYr_ncsr_local_group_50.0760.0514676
ELECTRON MICROSCOPYr_ncsr_local_group_60.0720.0514683
ELECTRON MICROSCOPYr_ncsr_local_group_70.0760.0514719
ELECTRON MICROSCOPYr_ncsr_local_group_80.0770.0514689
ELECTRON MICROSCOPYr_ncsr_local_group_90.0480.0514928
ELECTRON MICROSCOPYr_ncsr_local_group_100.0760.0514688
ELECTRON MICROSCOPYr_ncsr_local_group_110.0450.0514984
ELECTRON MICROSCOPYr_ncsr_local_group_120.0790.0514701
ELECTRON MICROSCOPYr_ncsr_local_group_130.0560.0514906
ELECTRON MICROSCOPYr_ncsr_local_group_140.0690.0514740
ELECTRON MICROSCOPYr_ncsr_local_group_150.0430.0514889
ELECTRON MICROSCOPYr_ncsr_local_group_160.0710.0514709
ELECTRON MICROSCOPYr_ncsr_local_group_170.0360.0514955
ELECTRON MICROSCOPYr_ncsr_local_group_180.0670.0514749
ELECTRON MICROSCOPYr_ncsr_local_group_190.0680.0514695
ELECTRON MICROSCOPYr_ncsr_local_group_200.030.0515033
ELECTRON MICROSCOPYr_ncsr_local_group_210.0710.0514752
ELECTRON MICROSCOPYr_ncsr_local_group_220.0350.0515027
ELECTRON MICROSCOPYr_ncsr_local_group_230.070.0514739
ELECTRON MICROSCOPYr_ncsr_local_group_240.0440.0514891
ELECTRON MICROSCOPYr_ncsr_local_group_250.0690.0514695
ELECTRON MICROSCOPYr_ncsr_local_group_260.0740.0514715
ELECTRON MICROSCOPYr_ncsr_local_group_270.0430.0514970
ELECTRON MICROSCOPYr_ncsr_local_group_280.0690.0514768
ELECTRON MICROSCOPYr_ncsr_local_group_290.0390.054721
ELECTRON MICROSCOPYr_ncsr_local_group_300.0320.054728
ELECTRON MICROSCOPYr_ncsr_local_group_310.0320.054716
ELECTRON MICROSCOPYr_ncsr_local_group_320.0290.054728
ELECTRON MICROSCOPYr_ncsr_local_group_330.0360.054726
ELECTRON MICROSCOPYr_ncsr_local_group_340.0310.054720
ELECTRON MICROSCOPYr_ncsr_local_group_350.0340.054722
ELECTRON MICROSCOPYr_ncsr_local_group_360.0270.054732
ELECTRON MICROSCOPYr_ncsr_local_group_370.0360.054705
ELECTRON MICROSCOPYr_ncsr_local_group_380.0410.054719
ELECTRON MICROSCOPYr_ncsr_local_group_390.040.054718
ELECTRON MICROSCOPYr_ncsr_local_group_400.040.054731
ELECTRON MICROSCOPYr_ncsr_local_group_410.0340.054726
ELECTRON MICROSCOPYr_ncsr_local_group_420.0270.054712
ELECTRON MICROSCOPYr_ncsr_local_group_430.0320.054738
ELECTRON MICROSCOPYr_ncsr_local_group_440.0290.054740
ELECTRON MICROSCOPYr_ncsr_local_group_450.0350.054737
ELECTRON MICROSCOPYr_ncsr_local_group_460.0270.054733
ELECTRON MICROSCOPYr_ncsr_local_group_470.0320.054720
ELECTRON MICROSCOPYr_ncsr_local_group_480.0370.054705
ELECTRON MICROSCOPYr_ncsr_local_group_490.0420.054700
ELECTRON MICROSCOPYr_ncsr_local_group_500.0380.054694
ELECTRON MICROSCOPYr_ncsr_local_group_510.0340.054735
ELECTRON MICROSCOPYr_ncsr_local_group_520.0340.054727
ELECTRON MICROSCOPYr_ncsr_local_group_530.0330.054725
ELECTRON MICROSCOPYr_ncsr_local_group_540.030.054740
ELECTRON MICROSCOPYr_ncsr_local_group_550.0230.054738
ELECTRON MICROSCOPYr_ncsr_local_group_560.0310.054742
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AELECTRON MICROSCOPYLocal ncs0.081480.0501
12CELECTRON MICROSCOPYLocal ncs0.081480.0501
23AELECTRON MICROSCOPYLocal ncs0.075360.0501
24EELECTRON MICROSCOPYLocal ncs0.075360.0501
35AELECTRON MICROSCOPYLocal ncs0.074060.0501
36FELECTRON MICROSCOPYLocal ncs0.074060.0501
47AELECTRON MICROSCOPYLocal ncs0.074350.0501
48IELECTRON MICROSCOPYLocal ncs0.074350.0501
59AELECTRON MICROSCOPYLocal ncs0.075870.0501
510JELECTRON MICROSCOPYLocal ncs0.075870.0501
611AELECTRON MICROSCOPYLocal ncs0.071730.0501
612MELECTRON MICROSCOPYLocal ncs0.071730.0501
713AELECTRON MICROSCOPYLocal ncs0.076420.0501
714NELECTRON MICROSCOPYLocal ncs0.076420.0501
815CELECTRON MICROSCOPYLocal ncs0.077050.0501
816EELECTRON MICROSCOPYLocal ncs0.077050.0501
917CELECTRON MICROSCOPYLocal ncs0.048110.05011
918FELECTRON MICROSCOPYLocal ncs0.048110.05011
1019CELECTRON MICROSCOPYLocal ncs0.076490.0501
1020IELECTRON MICROSCOPYLocal ncs0.076490.0501
1121CELECTRON MICROSCOPYLocal ncs0.044960.05011
1122JELECTRON MICROSCOPYLocal ncs0.044960.05011
1223CELECTRON MICROSCOPYLocal ncs0.07880.0501
1224MELECTRON MICROSCOPYLocal ncs0.07880.0501
1325CELECTRON MICROSCOPYLocal ncs0.055780.05011
1326NELECTRON MICROSCOPYLocal ncs0.055780.05011
1427EELECTRON MICROSCOPYLocal ncs0.069430.0501
1428FELECTRON MICROSCOPYLocal ncs0.069430.0501
1529EELECTRON MICROSCOPYLocal ncs0.043330.05011
1530IELECTRON MICROSCOPYLocal ncs0.043330.05011
1631EELECTRON MICROSCOPYLocal ncs0.071390.0501
1632JELECTRON MICROSCOPYLocal ncs0.071390.0501
1733EELECTRON MICROSCOPYLocal ncs0.035570.05011
1734MELECTRON MICROSCOPYLocal ncs0.035570.05011
1835EELECTRON MICROSCOPYLocal ncs0.066670.0501
1836NELECTRON MICROSCOPYLocal ncs0.066670.0501
1937FELECTRON MICROSCOPYLocal ncs0.068030.0501
1938IELECTRON MICROSCOPYLocal ncs0.068030.0501
2039FELECTRON MICROSCOPYLocal ncs0.029940.05011
2040JELECTRON MICROSCOPYLocal ncs0.029940.05011
2141FELECTRON MICROSCOPYLocal ncs0.071120.0501
2142MELECTRON MICROSCOPYLocal ncs0.071120.0501
2243FELECTRON MICROSCOPYLocal ncs0.034780.05011
2244NELECTRON MICROSCOPYLocal ncs0.034780.05011
2345IELECTRON MICROSCOPYLocal ncs0.069570.0501
2346JELECTRON MICROSCOPYLocal ncs0.069570.0501
2447IELECTRON MICROSCOPYLocal ncs0.043890.05011
2448MELECTRON MICROSCOPYLocal ncs0.043890.05011
2549IELECTRON MICROSCOPYLocal ncs0.068870.0501
2550NELECTRON MICROSCOPYLocal ncs0.068870.0501
2651JELECTRON MICROSCOPYLocal ncs0.073640.0501
2652MELECTRON MICROSCOPYLocal ncs0.073640.0501
2753JELECTRON MICROSCOPYLocal ncs0.04310.05011
2754NELECTRON MICROSCOPYLocal ncs0.04310.05011
2855MELECTRON MICROSCOPYLocal ncs0.068670.0501
2856NELECTRON MICROSCOPYLocal ncs0.068670.0501
2957BELECTRON MICROSCOPYLocal ncs0.039080.05012
2958DELECTRON MICROSCOPYLocal ncs0.039080.05012
3059BELECTRON MICROSCOPYLocal ncs0.031790.05012
3060GELECTRON MICROSCOPYLocal ncs0.031790.05012
3161BELECTRON MICROSCOPYLocal ncs0.031660.05011
3162HELECTRON MICROSCOPYLocal ncs0.031660.05011
3263BELECTRON MICROSCOPYLocal ncs0.028610.05012
3264KELECTRON MICROSCOPYLocal ncs0.028610.05012
3365BELECTRON MICROSCOPYLocal ncs0.035660.05012
3366LELECTRON MICROSCOPYLocal ncs0.035660.05012
3467BELECTRON MICROSCOPYLocal ncs0.030860.05012
3468OELECTRON MICROSCOPYLocal ncs0.030860.05012
3569BELECTRON MICROSCOPYLocal ncs0.03420.05012
3570PELECTRON MICROSCOPYLocal ncs0.03420.05012
3671DELECTRON MICROSCOPYLocal ncs0.026780.05012
3672GELECTRON MICROSCOPYLocal ncs0.026780.05012
3773DELECTRON MICROSCOPYLocal ncs0.035710.05012
3774HELECTRON MICROSCOPYLocal ncs0.035710.05012
3875DELECTRON MICROSCOPYLocal ncs0.041240.05012
3876KELECTRON MICROSCOPYLocal ncs0.041240.05012
3977DELECTRON MICROSCOPYLocal ncs0.039690.05012
3978LELECTRON MICROSCOPYLocal ncs0.039690.05012
4079DELECTRON MICROSCOPYLocal ncs0.04020.05012
4080OELECTRON MICROSCOPYLocal ncs0.04020.05012
4181DELECTRON MICROSCOPYLocal ncs0.033730.05012
4182PELECTRON MICROSCOPYLocal ncs0.033730.05012
4283GELECTRON MICROSCOPYLocal ncs0.027090.05012
4284HELECTRON MICROSCOPYLocal ncs0.027090.05012
4385GELECTRON MICROSCOPYLocal ncs0.032320.05012
4386KELECTRON MICROSCOPYLocal ncs0.032320.05012
4487GELECTRON MICROSCOPYLocal ncs0.028880.05012
4488LELECTRON MICROSCOPYLocal ncs0.028880.05012
4589GELECTRON MICROSCOPYLocal ncs0.034790.05012
4590OELECTRON MICROSCOPYLocal ncs0.034790.05012
4691GELECTRON MICROSCOPYLocal ncs0.026850.05012
4692PELECTRON MICROSCOPYLocal ncs0.026850.05012
4793HELECTRON MICROSCOPYLocal ncs0.032290.05012
4794KELECTRON MICROSCOPYLocal ncs0.032290.05012
4895HELECTRON MICROSCOPYLocal ncs0.036730.05012
4896LELECTRON MICROSCOPYLocal ncs0.036730.05012
4997HELECTRON MICROSCOPYLocal ncs0.041840.05012
4998OELECTRON MICROSCOPYLocal ncs0.041840.05012
5099HELECTRON MICROSCOPYLocal ncs0.038440.05012
50100PELECTRON MICROSCOPYLocal ncs0.038440.05012
51101KELECTRON MICROSCOPYLocal ncs0.034450.05012
51102LELECTRON MICROSCOPYLocal ncs0.034450.05012
52103KELECTRON MICROSCOPYLocal ncs0.034410.05012
52104OELECTRON MICROSCOPYLocal ncs0.034410.05012
53105KELECTRON MICROSCOPYLocal ncs0.033350.05012
53106PELECTRON MICROSCOPYLocal ncs0.033350.05012
54107LELECTRON MICROSCOPYLocal ncs0.029630.05012
54108OELECTRON MICROSCOPYLocal ncs0.029630.05012
55109LELECTRON MICROSCOPYLocal ncs0.022990.05012
55110PELECTRON MICROSCOPYLocal ncs0.022990.05012
56111OELECTRON MICROSCOPYLocal ncs0.03120.05012
56112PELECTRON MICROSCOPYLocal ncs0.03120.05012
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
2.26-2.3191.954354391.954354390.6011.954
2.319-2.3821.518345821.518345820.6871.518
2.382-2.4511.351335441.351335440.7511.351
2.451-2.5271.141326211.141326210.7991.141
2.527-2.610.97315940.97315940.8450.97
2.61-2.7010.764305360.764305360.8870.764
2.701-2.8030.597294320.597294320.9220.597
2.803-2.9170.451284500.451284500.9350.451
2.917-3.0470.328273120.328273120.9510.328
3.047-3.1960.222260220.222260220.9610.222
3.196-3.3690.163247440.163247440.9690.163
3.369-3.5730.142233760.142233760.9760.142
3.573-3.8190.169220230.169220230.9740.169
3.819-4.1250.186204200.186204200.9720.186
4.125-4.5180.213188370.213188370.9670.213
4.518-5.0510.218170490.218170490.9620.218
5.051-5.8310.233150060.233150060.9360.233
5.831-7.1380.281126820.281126820.8980.281
7.138-10.0820.30297660.30297660.8930.302
10.082-138.7870.41354330.41354330.9640.413

+
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