[English] 日本語
Yorodumi
- PDB-3p1m: Crystal structure of human ferredoxin-1 (FDX1) in complex with ir... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p1m
TitleCrystal structure of human ferredoxin-1 (FDX1) in complex with iron-sulfur cluster
ComponentsAdrenodoxin, mitochondrialAdrenal ferredoxin
KeywordsELECTRON TRANSPORT / Structural Genomics Consortium / SGC / Adrenodoxin / Ferredoxin / iron-sulfur cluster / Mitochondria
Function / homology
Function and homology information


Electron transport from NADPH to Ferredoxin / Defective CYP11A1 causes AICSR / Mitochondrial iron-sulfur cluster biogenesis / hormone biosynthetic process / P450-containing electron transport chain / Pregnenolone biosynthesis / steroid biosynthetic process / electron transport chain / Endogenous sterols / cellular response to forskolin ...Electron transport from NADPH to Ferredoxin / Defective CYP11A1 causes AICSR / Mitochondrial iron-sulfur cluster biogenesis / hormone biosynthetic process / P450-containing electron transport chain / Pregnenolone biosynthesis / steroid biosynthetic process / electron transport chain / Endogenous sterols / cellular response to forskolin / cellular response to cAMP / cholesterol metabolic process / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial matrix / iron ion binding / mitochondrion
Similarity search - Function
Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) ...Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / CITRATE ANION / : / Adrenodoxin, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsChaikuad, A. / Johansson, C. / Krojer, T. / Yue, W.W. / Phillips, C. / Bray, J.E. / Pike, A.C.W. / Muniz, J.R.C. / Vollmar, M. / Weigelt, J. ...Chaikuad, A. / Johansson, C. / Krojer, T. / Yue, W.W. / Phillips, C. / Bray, J.E. / Pike, A.C.W. / Muniz, J.R.C. / Vollmar, M. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Kavanagh, K. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human ferredoxin-1 (FDX1) in complex with iron-sulfur cluster
Authors: Chaikuad, A. / Johansson, C. / Krojer, T. / Yue, W.W. / Phillips, C. / Bray, J.E. / Pike, A.C.W. / Muniz, J.R.C. / Vollmar, M. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Authors: Chaikuad, A. / Johansson, C. / Krojer, T. / Yue, W.W. / Phillips, C. / Bray, J.E. / Pike, A.C.W. / Muniz, J.R.C. / Vollmar, M. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Kavanagh, K. / Oppermann, U.
History
DepositionSep 30, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_ncs_dom_lim / 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_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_conn.ptnr2_label_seq_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 / _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: Adrenodoxin, mitochondrial
B: Adrenodoxin, mitochondrial
C: Adrenodoxin, mitochondrial
D: Adrenodoxin, mitochondrial
E: Adrenodoxin, mitochondrial
F: Adrenodoxin, mitochondrial
G: Adrenodoxin, mitochondrial
H: Adrenodoxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,18335
Polymers116,5788
Non-polymers3,60527
Water4,666259
1
A: Adrenodoxin, mitochondrial
G: Adrenodoxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0459
Polymers29,1442
Non-polymers9007
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-17 kcal/mol
Surface area14260 Å2
MethodPISA
2
B: Adrenodoxin, mitochondrial
H: Adrenodoxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9538
Polymers29,1442
Non-polymers8086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-16 kcal/mol
Surface area13850 Å2
MethodPISA
3
C: Adrenodoxin, mitochondrial
F: Adrenodoxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0459
Polymers29,1442
Non-polymers9007
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-17 kcal/mol
Surface area14170 Å2
MethodPISA
4
D: Adrenodoxin, mitochondrial
E: Adrenodoxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1429
Polymers29,1442
Non-polymers9977
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-19 kcal/mol
Surface area13840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.576, 76.576, 234.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11F
21B
31D
41E
51G
61H
12E
22B
13H
23D
14G
24F
15A
25C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ILEILEVALVAL1FF67 - 1718 - 112
211ILEILEVALVAL1BB67 - 1718 - 112
311ILEILEVALVAL1DD67 - 1718 - 112
411ILEILEVALVAL1EE67 - 1718 - 112
511ILEILEVALVAL1GG67 - 1718 - 112
611ILEILEVALVAL1HH67 - 1718 - 112
112ALAALAGLNGLN5EE172 - 191113 - 132
212ALAALAGLNGLN5BB172 - 191113 - 132
113ALAALAGLNGLN5HH172 - 191113 - 132
213ALAALAGLNGLN5DD172 - 191113 - 132
114ALAALAALAALA5GG172 - 185113 - 126
214ALAALAALAALA5FF172 - 185113 - 126
115ILEILEVALVAL1AA67 - 1718 - 112
215ILEILEVALVAL1CC67 - 1718 - 112
125ALAALAALAALA5AA172 - 185113 - 126
225ALAALAALAALA5CC172 - 185113 - 126

NCS ensembles :
ID
1
2
3
4
5
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN.

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Adrenodoxin, mitochondrial / Adrenal ferredoxin / Adrenal ferredoxin / Ferredoxin-1 / Hepatoredoxin


Mass: 14572.235 Da / Num. of mol.: 8
Fragment: 2Fe-2S ferredoxin-type domain, UNP residues 61-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADX, FDX1 / Plasmid: pNIC-CTHF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: P10109

-
Non-polymers , 5 types, 286 molecules

#2: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 3.4 Å3/Da / Density % sol: 63.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1.75M Potassium Citrate (K3Cit), pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2009 / Details: Kirkpatrick Baez bimorph mirror pair
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.54→50.5 Å / Num. all: 50847 / Num. obs: 50786 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 53.4 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 11.6
Reflection shellResolution: 2.54→2.67 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 2 / Num. unique all: 7351 / % possible all: 99

-
Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CJE

1cje


Resolution: 2.54→43.91 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.917 / SU B: 18.286 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS DURING REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.24132 1971 3.9 %RANDOM
Rwork0.20395 ---
all0.20541 50786 --
obs0.20541 48817 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.327 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å2-0.54 Å20 Å2
2---1.08 Å20 Å2
3---1.62 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.54→43.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7733 0 169 259 8161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0217997
X-RAY DIFFRACTIONr_bond_other_d0.0020.025042
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.98110778
X-RAY DIFFRACTIONr_angle_other_deg0.933.00512363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92351009
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65825.652368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.765151352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6561540
X-RAY DIFFRACTIONr_chiral_restr0.0770.21290
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028931
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021465
X-RAY DIFFRACTIONr_mcbond_it0.4211.55032
X-RAY DIFFRACTIONr_mcbond_other0.111.52108
X-RAY DIFFRACTIONr_mcangle_it0.78628122
X-RAY DIFFRACTIONr_scbond_it2.00232965
X-RAY DIFFRACTIONr_scangle_it2.1944.52640
X-RAY DIFFRACTIONr_sphericity_free9.03338
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11F1276TIGHT POSITIONAL0.040.05
12B1276TIGHT POSITIONAL0.030.05
13D1276TIGHT POSITIONAL0.040.05
14E1276TIGHT POSITIONAL0.030.05
15G1276TIGHT POSITIONAL0.040.05
16H1276TIGHT POSITIONAL0.040.05
11F1276TIGHT THERMAL0.080.5
12B1276TIGHT THERMAL0.070.5
13D1276TIGHT THERMAL0.080.5
14E1276TIGHT THERMAL0.070.5
15G1276TIGHT THERMAL0.080.5
16H1276TIGHT THERMAL0.080.5
21E119MEDIUM POSITIONAL0.240.5
21E131LOOSE POSITIONAL0.875
21E119MEDIUM THERMAL0.282
21E131LOOSE THERMAL0.4110
31H119MEDIUM POSITIONAL0.110.5
31H139LOOSE POSITIONAL0.395
31H119MEDIUM THERMAL0.212
31H139LOOSE THERMAL0.3410
41G83MEDIUM POSITIONAL0.10.5
41G75LOOSE POSITIONAL0.455
41G83MEDIUM THERMAL0.62
41G75LOOSE THERMAL0.4310
51A1330TIGHT POSITIONAL0.110.05
51A83MEDIUM POSITIONAL0.060.5
51A80LOOSE POSITIONAL0.115
51A1330TIGHT THERMAL0.290.5
51A83MEDIUM THERMAL0.272
51A80LOOSE THERMAL0.4510
LS refinement shellResolution: 2.537→2.603 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 145 -
Rwork0.346 3528 -
obs--97.27 %
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)
18.166-0.09520.01371.0923-0.26541.0888-0.12080.72130.7222-0.51850.09890.0018-0.48820.15730.02190.634-0.151-0.05220.13050.04280.105216.597516.02342.3919
23.49681.93312.31342.6221.61022.96880.03690.0704-0.1341-0.298-0.0294-0.1130.00910.0925-0.00750.09310.0062-0.00380.01640.01530.028420.921812.411916.8495
33.2562.51060.52453.221-2.05935.29760.3322-0.1221-0.26180.5155-0.1325-0.3363-0.40170.1286-0.19970.25340.0633-0.02820.34260.10450.46378.006115.843285.091
44.51831.5021-2.05113.69320.39015.90820.1337-0.30360.34520.17950.07370.2901-0.5184-0.5079-0.20740.06450.07310.02740.30110.17320.215169.841916.249275.7246
56.70670.1843-9.87450.2904-0.621916.0925-0.27460.617-0.47360.0145-0.1066-0.1054-0.0097-0.73240.38130.1994-0.13180.05050.30760.15220.396692.766113.043958.1356
62.7141-2.3190.2617.5672-0.58341.55030.0736-0.65110.32660.9456-0.1158-0.6379-0.39850.31010.04220.2688-0.2194-0.06510.34870.00520.114643.814944.360846.4303
71.06630.4968-0.32235.1462-2.84742.97450.0548-0.25440.00520.1023-0.08030.1191-0.0458-0.06990.02550.0289-0.0342-0.01450.08940.0060.02138.582146.438731.8074
84.0587-1.42232.20013.51670.09347.69950.3498-0.0983-0.7270.1785-0.09990.32570.6735-0.3675-0.24990.2643-0.049-0.01160.23060.19160.488951.7695-10.218268.541
93.994-1.87462.65821.641-1.57762.91270.18570.0604-0.269-0.1359-0.03250.00120.28770.1827-0.15330.1064-0.0386-0.0160.19280.13120.185653.11182.981662.0753
103.1554-3.1771-0.2595.512-3.15245.85460.28260.18240.2186-0.5969-0.1238-0.50330.48520.0496-0.15880.2303-0.0479-0.00660.32850.03860.509939.37966.220541.4136
114.1658-0.95282.21362.06670.66455.31980.11670.2104-0.3729-0.10220.10910.34730.5153-0.5093-0.22580.0823-0.092-0.03320.31320.19450.246631.66295.859951.2453
126.4021-0.18567.32860.6321-0.951710.2764-0.3863-0.57250.37210.12090.0919-0.112-0.4659-0.46390.29440.07010.1223-0.01160.30530.07990.326554.41639.140968.3544
133.7803-1.2004-0.03312.5133-2.874.14310.11570.1021-0.12950.22510.28860.5586-0.3136-0.62-0.40440.1719-0.02790.02310.2908-0.09590.51965.72413.333129.8818
142.24180.5134-0.32525.8709-1.08621.39140.0673-0.20730.3520.1118-0.07360.1497-0.1845-0.06790.00630.0533-0.0338-0.01450.1096-0.0180.070877.8908-0.959228.4068
150.62423.424-2.740726.3038-31.674948.93790.58220.2867-0.4012.37490.0463-1.0706-0.32431.9583-0.62850.90610.4003-0.3630.6722-0.25531.081891.443-40.963933.0246
163.7919-0.94842.93813.06041.95835.05440.07460.2265-0.55450.16670.3399-0.15770.43280.5656-0.41450.3620.05780.17380.1869-0.01340.572146.603314.31318.7401
175.32462.24570.64013.53820.65071.53060.02670.1004-0.0234-0.1730.0227-0.4247-0.07110.1964-0.04940.11960.01410.01920.03470.00910.076536.793722.722420.3388
1818.3056-0.1192-9.76957.49598.103830.8387-0.04492.2926-0.0998-0.29140.26611.6383-1.7297-1.8088-0.22120.49110.27520.07050.52710.19810.689-4.999514.248815.7235
194.32921.2567-2.33693.0873-0.36526.27960.29210.16660.7221-0.1509-0.01450.4469-0.8394-0.357-0.27760.27120.05020.00210.23420.18980.469713.832.609958.2607
204.72042.1671-3.11841.8706-1.88862.96020.1894-0.00810.26620.1406-0.0545-0.0101-0.25720.1367-0.13490.10280.0319-0.00190.17610.12110.165214.671618.939564.8148
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A66 - 113
2X-RAY DIFFRACTION2A114 - 191
3X-RAY DIFFRACTION3B66 - 113
4X-RAY DIFFRACTION4B114 - 165
5X-RAY DIFFRACTION5B166 - 191
6X-RAY DIFFRACTION6C65 - 113
7X-RAY DIFFRACTION7C114 - 191
8X-RAY DIFFRACTION8D65 - 113
9X-RAY DIFFRACTION9D114 - 191
10X-RAY DIFFRACTION10E65 - 113
11X-RAY DIFFRACTION11E114 - 165
12X-RAY DIFFRACTION12E166 - 191
13X-RAY DIFFRACTION13F64 - 113
14X-RAY DIFFRACTION14F114 - 184
15X-RAY DIFFRACTION15F185 - 191
16X-RAY DIFFRACTION16G64 - 113
17X-RAY DIFFRACTION17G114 - 184
18X-RAY DIFFRACTION18G185 - 191
19X-RAY DIFFRACTION19H64 - 113
20X-RAY DIFFRACTION20H114 - 191

+
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