[English] 日本語
Yorodumi
- PDB-7c3f: Crystal structure of ferredoxin: thioredoxin reductase and thiore... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7c3f
TitleCrystal structure of ferredoxin: thioredoxin reductase and thioredoxin m2 complex
Components
  • (Ferredoxin-thioredoxin reductase ...) x 2
  • Thioredoxin M2, chloroplastic
KeywordsELECTRON TRANSPORT / FTR / Trx m2
Function / homology
Function and homology information


ferredoxin-thioredoxin reductase activity / ferredoxin:thioredoxin reductase / oxidoreductase activity, acting on iron-sulfur proteins as donors / thylakoid / positive regulation of catalytic activity / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / protein-disulfide reductase activity / photosynthesis ...ferredoxin-thioredoxin reductase activity / ferredoxin:thioredoxin reductase / oxidoreductase activity, acting on iron-sulfur proteins as donors / thylakoid / positive regulation of catalytic activity / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / protein-disulfide reductase activity / photosynthesis / enzyme activator activity / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / metal ion binding / cytosol
Similarity search - Function
Ferredoxin Thioredoxin Reductase / Ferredoxin thioredoxin reductase catalytic beta subunit / Ferredoxin thioredoxin reductase, alpha chain / Ferredoxin-thioredoxin reductase, variable chain / Ferredoxin thioredoxin reductase variable alpha chain / Ferredoxin thioredoxin reductase catalytic beta subunit / Ferredoxin thioredoxin reductase catalytic beta subunit superfamily / Ferredoxin thioredoxin reductase catalytic beta chain / Thioredoxin / Electron transport accessory-like domain superfamily ...Ferredoxin Thioredoxin Reductase / Ferredoxin thioredoxin reductase catalytic beta subunit / Ferredoxin thioredoxin reductase, alpha chain / Ferredoxin-thioredoxin reductase, variable chain / Ferredoxin thioredoxin reductase variable alpha chain / Ferredoxin thioredoxin reductase catalytic beta subunit / Ferredoxin thioredoxin reductase catalytic beta subunit superfamily / Ferredoxin thioredoxin reductase catalytic beta chain / Thioredoxin / Electron transport accessory-like domain superfamily / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Ferredoxin-thioredoxin reductase subunit A2, chloroplastic / Thioredoxin M2, chloroplastic / Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3986 Å
AuthorsKurisu, G. / Juniar, L. / Tanaka, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16H06560 Japan
CitationJournal: Protein Sci. / Year: 2020
Title: Structural basis for thioredoxin isoform-based fine-tuning of ferredoxin-thioredoxin reductase activity.
Authors: Juniar, L. / Tanaka, H. / Yoshida, K. / Hisabori, T. / Kurisu, G.
History
DepositionMay 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic
B: Ferredoxin-thioredoxin reductase variable chain, chloroplastic
C: Thioredoxin M2, chloroplastic
D: Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic
E: Ferredoxin-thioredoxin reductase variable chain, chloroplastic
F: Thioredoxin M2, chloroplastic
G: Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic
H: Ferredoxin-thioredoxin reductase variable chain, chloroplastic
I: Thioredoxin M2, chloroplastic
J: Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic
K: Ferredoxin-thioredoxin reductase variable chain, chloroplastic
L: Thioredoxin M2, chloroplastic
M: Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic
N: Ferredoxin-thioredoxin reductase variable chain, chloroplastic
O: Thioredoxin M2, chloroplastic
P: Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic
Q: Ferredoxin-thioredoxin reductase variable chain, chloroplastic
R: Thioredoxin M2, chloroplastic
S: Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic
T: Ferredoxin-thioredoxin reductase variable chain, chloroplastic
U: Thioredoxin M2, chloroplastic
W: Thioredoxin M2, chloroplastic
V: Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,85540
Polymers292,16423
Non-polymers2,69117
Water9,548530
1
A: Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic
B: Ferredoxin-thioredoxin reductase variable chain, chloroplastic
C: Thioredoxin M2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4916
Polymers38,0933
Non-polymers3983
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic
E: Ferredoxin-thioredoxin reductase variable chain, chloroplastic
F: Thioredoxin M2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4916
Polymers38,0933
Non-polymers3983
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic
H: Ferredoxin-thioredoxin reductase variable chain, chloroplastic
I: Thioredoxin M2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4685
Polymers38,0933
Non-polymers3752
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic
K: Ferredoxin-thioredoxin reductase variable chain, chloroplastic
L: Thioredoxin M2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4916
Polymers38,0933
Non-polymers3983
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
M: Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic
N: Ferredoxin-thioredoxin reductase variable chain, chloroplastic
O: Thioredoxin M2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4916
Polymers38,0933
Non-polymers3983
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
P: Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic
Q: Ferredoxin-thioredoxin reductase variable chain, chloroplastic
R: Thioredoxin M2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4685
Polymers38,0933
Non-polymers3752
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
S: Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic
T: Ferredoxin-thioredoxin reductase variable chain, chloroplastic
U: Thioredoxin M2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4454
Polymers38,0933
Non-polymers3521
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
W: Thioredoxin M2, chloroplastic
V: Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic


Theoretical massNumber of molelcules
Total (without water)25,5102
Polymers25,5102
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.262, 137.209, 192.457
Angle α, β, γ (deg.)90.000, 90.210, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 98 or resid 100 through 115 or resid 399))
21(chain D and (resid 3 through 98 or resid 100 through 115 or resid 399))
31(chain G and (resid 3 through 98 or resid 100 through 115 or resid 399))
41(chain J and (resid 3 through 98 or resid 100 through 115 or resid 399))
51(chain M and (resid 3 through 98 or resid 100 through 115 or resid 399))
61(chain P and (resid 3 through 115 or resid 399))
71(chain S and (resid 3 through 98 or resid 100 through 115 or resid 399))
12(chain B and (resid 24 through 107 or resid 109 through 111))
22(chain E and (resid 24 through 107 or resid 109 through 111))
32(chain H and (resid 24 through 107 or resid 109 through 111))
42(chain K and (resid 24 through 107 or resid 109 through 111))
52(chain N and (resid 24 through 107 or resid 109 through 111))
62(chain Q and (resid 24 through 107 or resid 109 through 111))
72chain T
13(chain C and (resid 16 through 68 or resid 70...
23(chain F and (resid 16 through 68 or resid 70...
33(chain I and (resid 16 through 68 or resid 70...
43(chain L and (resid 16 through 68 or resid 70...
53(chain O and (resid 16 through 68 or resid 70...
63(chain R and (resid 16 through 68 or resid 70...
73(chain U and (resid 16 through 68 or resid 70...
83chain W

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 through 98 or resid 100 through 115 or resid 399))A3 - 98
121(chain A and (resid 3 through 98 or resid 100 through 115 or resid 399))A100 - 115
131(chain A and (resid 3 through 98 or resid 100 through 115 or resid 399))A399
211(chain D and (resid 3 through 98 or resid 100 through 115 or resid 399))D3 - 98
221(chain D and (resid 3 through 98 or resid 100 through 115 or resid 399))D100 - 115
231(chain D and (resid 3 through 98 or resid 100 through 115 or resid 399))D399
311(chain G and (resid 3 through 98 or resid 100 through 115 or resid 399))G3 - 98
321(chain G and (resid 3 through 98 or resid 100 through 115 or resid 399))G100 - 115
331(chain G and (resid 3 through 98 or resid 100 through 115 or resid 399))G399
411(chain J and (resid 3 through 98 or resid 100 through 115 or resid 399))J3 - 98
421(chain J and (resid 3 through 98 or resid 100 through 115 or resid 399))J100 - 115
431(chain J and (resid 3 through 98 or resid 100 through 115 or resid 399))J399
511(chain M and (resid 3 through 98 or resid 100 through 115 or resid 399))M3 - 98
521(chain M and (resid 3 through 98 or resid 100 through 115 or resid 399))M100 - 115
531(chain M and (resid 3 through 98 or resid 100 through 115 or resid 399))M399
611(chain P and (resid 3 through 115 or resid 399))P0
711(chain S and (resid 3 through 98 or resid 100 through 115 or resid 399))S3 - 98
721(chain S and (resid 3 through 98 or resid 100 through 115 or resid 399))S100 - 115
731(chain S and (resid 3 through 98 or resid 100 through 115 or resid 399))S399
112(chain B and (resid 24 through 107 or resid 109 through 111))B24 - 107
122(chain B and (resid 24 through 107 or resid 109 through 111))B109 - 111
212(chain E and (resid 24 through 107 or resid 109 through 111))E24 - 107
222(chain E and (resid 24 through 107 or resid 109 through 111))E109 - 111
312(chain H and (resid 24 through 107 or resid 109 through 111))H24 - 107
322(chain H and (resid 24 through 107 or resid 109 through 111))H109 - 111
412(chain K and (resid 24 through 107 or resid 109 through 111))K24 - 107
422(chain K and (resid 24 through 107 or resid 109 through 111))K109 - 111
512(chain N and (resid 24 through 107 or resid 109 through 111))N24 - 107
522(chain N and (resid 24 through 107 or resid 109 through 111))N109 - 111
612(chain Q and (resid 24 through 107 or resid 109 through 111))Q24 - 107
622(chain Q and (resid 24 through 107 or resid 109 through 111))Q109 - 111
712chain TT24 - 111
113(chain C and (resid 16 through 68 or resid 70...C16 - 68
123(chain C and (resid 16 through 68 or resid 70...C70 - 84
133(chain C and (resid 16 through 68 or resid 70...C87 - 113
143(chain C and (resid 16 through 68 or resid 70...C115 - 116
153(chain C and (resid 16 through 68 or resid 70...C118
213(chain F and (resid 16 through 68 or resid 70...F16 - 68
223(chain F and (resid 16 through 68 or resid 70...F70 - 84
233(chain F and (resid 16 through 68 or resid 70...F87 - 113
243(chain F and (resid 16 through 68 or resid 70...F115 - 116
253(chain F and (resid 16 through 68 or resid 70...F118
313(chain I and (resid 16 through 68 or resid 70...I16 - 68
323(chain I and (resid 16 through 68 or resid 70...I70 - 84
333(chain I and (resid 16 through 68 or resid 70...I87 - 113
343(chain I and (resid 16 through 68 or resid 70...I115 - 116
353(chain I and (resid 16 through 68 or resid 70...I118
413(chain L and (resid 16 through 68 or resid 70...L16 - 68
423(chain L and (resid 16 through 68 or resid 70...L70 - 84
433(chain L and (resid 16 through 68 or resid 70...L87 - 113
443(chain L and (resid 16 through 68 or resid 70...L115 - 116
453(chain L and (resid 16 through 68 or resid 70...L118
513(chain O and (resid 16 through 68 or resid 70...O16 - 68
523(chain O and (resid 16 through 68 or resid 70...O70 - 84
533(chain O and (resid 16 through 68 or resid 70...O87 - 113
543(chain O and (resid 16 through 68 or resid 70...O115 - 116
553(chain O and (resid 16 through 68 or resid 70...O118
613(chain R and (resid 16 through 68 or resid 70...R16 - 68
623(chain R and (resid 16 through 68 or resid 70...R70 - 84
633(chain R and (resid 16 through 68 or resid 70...R87 - 113
643(chain R and (resid 16 through 68 or resid 70...R115 - 116
653(chain R and (resid 16 through 68 or resid 70...R118
713(chain U and (resid 16 through 68 or resid 70...U16 - 68
723(chain U and (resid 16 through 68 or resid 70...U70 - 84
733(chain U and (resid 16 through 68 or resid 70...U87 - 113
743(chain U and (resid 16 through 68 or resid 70...U115 - 116
753(chain U and (resid 16 through 68 or resid 70...U118
813chain WW10 - 112

NCS ensembles :
ID
1
2
3
DetailsThe crystal contact is not so tight packed and there is space which is enough for two molecules and they turned out to be FTR catalytic (FTRC) and Trxm2cs.

-
Components

-
Ferredoxin-thioredoxin reductase ... , 2 types, 15 molecules ADGJMPSVBEHKNQT

#1: Protein
Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic / FTR-C / Ferredoxin-thioredoxin reductase subunit B / FTR-B


Mass: 12995.734 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Cell: chloroplast / Gene: FTRC / Plasmid: pETDUET1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q9SJ89, ferredoxin:thioredoxin reductase
#2: Protein
Ferredoxin-thioredoxin reductase variable chain, chloroplastic / Ferredoxin/thioredoxin reductase subunit A (Variable subunit) 2 / Putative lipoic acid synthase


Mass: 12583.467 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Cell: chloroplast
Gene: FTRA2, ferredoxin, At5g08410, At5g08410/F8L15_140, C24_LOCUS21561, F8L15.14
Plasmid: pETDUET1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8LBP6

-
Protein , 1 types, 8 molecules CFILORUW

#3: Protein
Thioredoxin M2, chloroplastic / AtTrxm2


Mass: 12514.233 Da / Num. of mol.: 8 / Mutation: C41S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Cell: Chloroplast / Gene: TRXM2, At4g03520, F9H3.15, T5L23.1 / Plasmid: pET23 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9SEU8

-
Non-polymers , 3 types, 547 molecules

#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.94 Å3/Da / Density % sol: 71.9 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 100 mM NaCitrate pH 6.2 18% PEG 3,350 / PH range: 6.2-7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3986→43.5724 Å / Num. obs: 175388 / % possible obs: 99.14 % / Redundancy: 3.8 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.1234 / Rpim(I) all: 0.07366 / Rrim(I) all: 0.1439 / Net I/σ(I): 8.82
Reflection shellResolution: 2.3986→2.485 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.406 / Mean I/σ(I) obs: 1.19 / Num. unique obs: 17050 / CC1/2: 0.493 / CC star: 0.813 / Rpim(I) all: 0.83 / Rrim(I) all: 1.635 / % possible all: 96.86

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2puk

2puk


Resolution: 2.3986→43.5724 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2447 8764 5 %
Rwork0.2095 166512 -
obs0.2112 175276 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 172.48 Å2 / Biso mean: 67.2192 Å2 / Biso min: 27.08 Å2
Refinement stepCycle: final / Resolution: 2.3986→43.5724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18397 0 66 530 18993
Biso mean--46.26 55.32 -
Num. residues----2328
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2352X-RAY DIFFRACTION11.894TORSIONAL
12D2352X-RAY DIFFRACTION11.894TORSIONAL
13G2352X-RAY DIFFRACTION11.894TORSIONAL
14J2352X-RAY DIFFRACTION11.894TORSIONAL
15M2352X-RAY DIFFRACTION11.894TORSIONAL
16P2352X-RAY DIFFRACTION11.894TORSIONAL
17S2352X-RAY DIFFRACTION11.894TORSIONAL
21B1813X-RAY DIFFRACTION11.894TORSIONAL
22E1813X-RAY DIFFRACTION11.894TORSIONAL
23H1813X-RAY DIFFRACTION11.894TORSIONAL
24K1813X-RAY DIFFRACTION11.894TORSIONAL
25N1813X-RAY DIFFRACTION11.894TORSIONAL
26Q1813X-RAY DIFFRACTION11.894TORSIONAL
27T1813X-RAY DIFFRACTION11.894TORSIONAL
31C2229X-RAY DIFFRACTION11.894TORSIONAL
32F2229X-RAY DIFFRACTION11.894TORSIONAL
33I2229X-RAY DIFFRACTION11.894TORSIONAL
34L2229X-RAY DIFFRACTION11.894TORSIONAL
35O2229X-RAY DIFFRACTION11.894TORSIONAL
36R2229X-RAY DIFFRACTION11.894TORSIONAL
37U2229X-RAY DIFFRACTION11.894TORSIONAL
38W2229X-RAY DIFFRACTION11.894TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3986-2.42580.35672620.3368496989
2.4258-2.45440.36352940.33135589100
2.4544-2.48430.37012920.31285553100
2.4843-2.51580.3282930.3069555599
2.5158-2.54880.33482910.29375525100
2.5488-2.58380.33052940.30015590100
2.5838-2.62070.35922910.29595543100
2.6207-2.65980.34192910.27655529100
2.6598-2.70130.30572970.26635626100
2.7013-2.74560.30612910.2655546100
2.7456-2.7930.31072930.26175553100
2.793-2.84370.31192950.26595603100
2.8437-2.89840.28652910.25965530100
2.8984-2.95760.31142930.25725567100
2.9576-3.02190.29142940.24355592100
3.0219-3.09210.27982950.22555594100
3.0921-3.16940.25222950.22285607100
3.1694-3.25510.26862930.225565100
3.2551-3.35090.27652930.23545584100
3.3509-3.4590.262930.22395550100
3.459-3.58250.25422940.2155590100
3.5825-3.72590.24592920.19695554100
3.7259-3.89540.21032930.1866556299
3.8954-4.10060.21612940.18559699
4.1006-4.35730.20712930.1704555899
4.3573-4.69340.20052920.1699554899
4.6934-5.1650.20762930.1716556799
5.165-5.91080.21082960.1847561799
5.9108-7.4410.20672950.1908561999
7.441-43.57240.1962910.1731553196

+
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