[English] 日本語
Yorodumi
- PDB-6i4z: Crystal structure of the disease-causing P453L mutant of the huma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6i4z
TitleCrystal structure of the disease-causing P453L mutant of the human dihydrolipoamide dehydrogenase
ComponentsDihydrolipoyl dehydrogenase, mitochondrialDihydrolipoamide dehydrogenase
KeywordsOXIDOREDUCTASE / Lipoamide dehydrogenase / Pathogenic mutation / E3 deficiency / Alpha-ketoglutarate dehydrogenase complex / 2-oxoglutarate dehydrogenase complex / Pyruvate dehydrogenase complex
Function / homology
Function and homology information


acetyltransferase complex / acrosomal matrix / Glycine degradation / : / oxoglutarate dehydrogenase complex / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / : / Lysine catabolism / acetyl-CoA biosynthetic process from pyruvate ...acetyltransferase complex / acrosomal matrix / Glycine degradation / : / oxoglutarate dehydrogenase complex / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / : / Lysine catabolism / acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase complex / branched-chain amino acid catabolic process / : / Citric acid cycle (TCA cycle) / Branched-chain amino acid catabolism / Pyruvate metabolism / Glyoxylate metabolism and glycine degradation / Regulation of pyruvate dehydrogenase (PDH) complex / motile cilium / sperm capacitation / Signaling by Retinoic Acid / mitochondrial electron transport, NADH to ubiquinone / gastrulation / regulation of membrane potential / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion / proteolysis / nucleus
Similarity search - Function
Dihydrolipoamide dehydrogenase / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase ...Dihydrolipoamide dehydrogenase / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Dihydrolipoyl dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.342 Å
AuthorsSzabo, E. / Wilk, P. / Torocsik, B. / Weiss, M.S. / Adam-Vizi, V. / Ambrus, A.
Funding support Hungary, United States, Germany, 10items
OrganizationGrant numberCountry
Hungarian Academy of Sciences02001 [to A.-V.V.] Hungary
Hungarian Scientific Research Fund, grant#112230 [to A.-V.V.] Hungary
Hungarian Brain Research Program, grant#KTIA_13_NAP_III/6 and 2017-1.2.1-NKP-2017-00002 [to A.-V.V.] Hungary
Hungarian Academy of SciencesBolyai Fellowship [to A.A.] Hungary
European Molecular Biology OrganizationShort-term Fellowship [to A.A.] Hungary
Semmelweis University, Young Investigator Research Grant [to A.A.] Hungary
Gedeon Richter PIc., Young Investigator Research Grant [to A.A.] Hungary
Fulbright Commission, Fulbright Fellowship [to A.A.] United States
European Union and Government of Hungary, grant#EFOP-3.6.3-VEKOP-16-2017-00009 [to S.E.] Hungary
European Union CALIPSOplus, grant#16204087-ST [to S.E. and A.A.] Germany
CitationJournal: Hum.Mol.Genet. / Year: 2019
Title: Underlying molecular alterations in human dihydrolipoamide dehydrogenase deficiency revealed by structural analyses of disease-causing enzyme variants.
Authors: Szabo, E. / Wilk, P. / Nagy, B. / Zambo, Z. / Bui, D. / Weichsel, A. / Arjunan, P. / Torocsik, B. / Hubert, A. / Furey, W. / Montfort, W.R. / Jordan, F. / Weiss, M.S. / Adam-Vizi, V. / Ambrus, A.
History
DepositionNov 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydrolipoyl dehydrogenase, mitochondrial
B: Dihydrolipoyl dehydrogenase, mitochondrial
C: Dihydrolipoyl dehydrogenase, mitochondrial
D: Dihydrolipoyl dehydrogenase, mitochondrial
E: Dihydrolipoyl dehydrogenase, mitochondrial
F: Dihydrolipoyl dehydrogenase, mitochondrial
G: Dihydrolipoyl dehydrogenase, mitochondrial
H: Dihydrolipoyl dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)430,10443
Polymers421,2268
Non-polymers8,87835
Water8,143452
1
A: Dihydrolipoyl dehydrogenase, mitochondrial
B: Dihydrolipoyl dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,55011
Polymers105,3062
Non-polymers2,2449
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11880 Å2
ΔGint-138 kcal/mol
Surface area35950 Å2
MethodPISA
2
C: Dihydrolipoyl dehydrogenase, mitochondrial
D: Dihydrolipoyl dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,83814
Polymers105,3062
Non-polymers2,53212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12380 Å2
ΔGint-167 kcal/mol
Surface area35720 Å2
MethodPISA
3
E: Dihydrolipoyl dehydrogenase, mitochondrial
F: Dihydrolipoyl dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,3589
Polymers105,3062
Non-polymers2,0517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-124 kcal/mol
Surface area35780 Å2
MethodPISA
4
G: Dihydrolipoyl dehydrogenase, mitochondrial
H: Dihydrolipoyl dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,3589
Polymers105,3062
Non-polymers2,0517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11410 Å2
ΔGint-122 kcal/mol
Surface area35680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.560, 123.390, 158.410
Angle α, β, γ (deg.)105.950, 91.310, 90.000
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 331 or resid 333 through 474 or resid 500))
21(chain B and (resid 3 through 331 or resid 333 through 474 or resid 500))
31(chain C and (resid 3 through 331 or resid 333 through 474 or resid 500))
41(chain D and (resid 3 through 331 or resid 333 through 474 or resid 500))
51(chain E and (resid 3 through 331 or resid 333 through 474 or resid 500))
61(chain F and (resid 3 through 331 or resid 333 through 474 or resid 500))
71(chain G and (resid 3 through 331 or resid 333 through 474 or resid 500))
81(chain H and (resid 3 through 331 or resid 333 through 474 or resid 500))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 through 331 or resid 333 through 474 or resid 500))A3 - 331
121(chain A and (resid 3 through 331 or resid 333 through 474 or resid 500))A333 - 474
131(chain A and (resid 3 through 331 or resid 333 through 474 or resid 500))A500
211(chain B and (resid 3 through 331 or resid 333 through 474 or resid 500))B3 - 331
221(chain B and (resid 3 through 331 or resid 333 through 474 or resid 500))B333 - 474
231(chain B and (resid 3 through 331 or resid 333 through 474 or resid 500))B500
311(chain C and (resid 3 through 331 or resid 333 through 474 or resid 500))C3 - 331
321(chain C and (resid 3 through 331 or resid 333 through 474 or resid 500))C333 - 474
331(chain C and (resid 3 through 331 or resid 333 through 474 or resid 500))C500
411(chain D and (resid 3 through 331 or resid 333 through 474 or resid 500))D3 - 331
421(chain D and (resid 3 through 331 or resid 333 through 474 or resid 500))D333 - 474
431(chain D and (resid 3 through 331 or resid 333 through 474 or resid 500))D500
511(chain E and (resid 3 through 331 or resid 333 through 474 or resid 500))E3 - 331
521(chain E and (resid 3 through 331 or resid 333 through 474 or resid 500))E333 - 474
531(chain E and (resid 3 through 331 or resid 333 through 474 or resid 500))E500
611(chain F and (resid 3 through 331 or resid 333 through 474 or resid 500))F3 - 331
621(chain F and (resid 3 through 331 or resid 333 through 474 or resid 500))F333 - 474
631(chain F and (resid 3 through 331 or resid 333 through 474 or resid 500))F500
711(chain G and (resid 3 through 331 or resid 333 through 474 or resid 500))G3 - 331
721(chain G and (resid 3 through 331 or resid 333 through 474 or resid 500))G333 - 474
731(chain G and (resid 3 through 331 or resid 333 through 474 or resid 500))G500
811(chain H and (resid 3 through 331 or resid 333 through 474 or resid 500))H3 - 331
821(chain H and (resid 3 through 331 or resid 333 through 474 or resid 500))H333 - 474
831(chain H and (resid 3 through 331 or resid 333 through 474 or resid 500))H500

-
Components

#1: Protein
Dihydrolipoyl dehydrogenase, mitochondrial / Dihydrolipoamide dehydrogenase / Dihydrolipoamide dehydrogenase / Glycine cleavage system L protein


Mass: 52653.215 Da / Num. of mol.: 8 / Mutation: P453L
Source method: isolated from a genetically manipulated source
Details: Sequence of the Strep-tag with the linker amino acids: MASWSHPQFEKGALEVLFQGPG
Source: (gene. exp.) Homo sapiens (human) / Gene: DLD, GCSL, LAD, PHE3 / Plasmid: pET52b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09622, dihydrolipoyl dehydrogenase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 2 M ammonium sulfate, 1.5 (v/v)% PEG 400, 0.1 M Hepes (pH7.3)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.34→46.567 Å / Num. obs: 164477 / % possible obs: 96.6 % / Redundancy: 4.972 % / Biso Wilson estimate: 47.64 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.144 / Rrim(I) all: 0.161 / Χ2: 0.97 / Net I/σ(I): 7.45
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.34-2.43.6010.9721.22107870.6021.13485.6
2.4-2.473.7370.8271.47115720.6690.96194.6
2.47-2.543.7310.6911.73113570.7520.80494.8
2.54-2.625.3530.6572.29115350.8380.72999.5
2.62-2.75.2770.5352.79111060.8740.59499.2
2.7-2.84.910.4213.34106950.9070.47198
2.8-2.95.5870.3554.25104770.9480.39199.6
2.9-3.025.5820.2795.35100260.9650.30899.5
3.02-3.165.5410.2276.5596170.9740.25199.6
3.16-3.315.4970.1758.392390.9830.19499.5
3.31-3.495.3520.1459.8787320.9850.16199.1
3.49-3.74.4560.13810.4173970.9760.15888.5
3.7-3.965.3630.12612.2571300.9880.1491.2
3.96-4.285.4930.09415.772170.9910.10499.3
4.28-4.685.3550.08517.4266370.9920.09499.3
4.68-5.245.0360.08616.3959430.990.09698.9
5.24-6.055.270.0915.9352530.9930.198
6.05-7.415.5340.08617.0444780.9930.09599.5
7.41-10.474.9440.06719.8434230.9950.07597.5
10.47-46.5675.1260.05821.3318560.9960.06497.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.586
Highest resolutionLowest resolution
Rotation46.57 Å2.76 Å

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZMD

1zmd


Resolution: 2.342→46.567 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 28.01
Details: TLS groups, NCS torsion-angle restraints and occupancy refinement were included, hydrogen atoms were added to the final model during refinement
RfactorNum. reflection% reflection
Rfree0.249 2465 1.5 %
Rwork0.2272 --
obs0.2276 164323 96.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 173.35 Å2 / Biso mean: 64.3838 Å2 / Biso min: 15.98 Å2
Refinement stepCycle: final / Resolution: 2.342→46.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28064 0 807 452 29323
Biso mean--55.03 45.04 -
Num. residues----3776
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A17708X-RAY DIFFRACTION14.242TORSIONAL
12B17708X-RAY DIFFRACTION14.242TORSIONAL
13C17708X-RAY DIFFRACTION14.242TORSIONAL
14D17708X-RAY DIFFRACTION14.242TORSIONAL
15E17708X-RAY DIFFRACTION14.242TORSIONAL
16F17708X-RAY DIFFRACTION14.242TORSIONAL
17G17708X-RAY DIFFRACTION14.242TORSIONAL
18H17708X-RAY DIFFRACTION14.242TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.342-2.3870.31841170.30957633775082
2.387-2.43580.31981340.2998827896195
2.4358-2.48870.30941350.28568854898995
2.4887-2.54660.30151350.28328848898395
2.5466-2.61030.28311410.269492579398100
2.6103-2.68090.32181410.26649258939999
2.6809-2.75970.26871400.25519182932298
2.7597-2.84880.27081390.24829134927399
2.8488-2.95060.30091410.253193289469100
2.9506-3.06870.29111420.254292939435100
3.0687-3.20840.27981400.245892299369100
3.2084-3.37750.27441420.23679298944099
3.3775-3.5890.25471390.22129121926099
3.589-3.8660.32211190.28427890800984
3.866-4.25480.20641400.19629193933398
4.2548-4.86990.1861400.16689191933199
4.8699-6.13340.22941400.19449211935198
6.1334-46.57640.18011400.19379111925198
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3792-0.5745-0.12171.20810.38890.3584-0.09560.30180.05790.19680.0487-0.17650.12410.0102-0.20830.05570.00710.00520.46370.03690.388118.1685-7.0516-7.7046
21.5987-0.44420.05522.52690.35141.8193-0.23120.14020.29250.761-0.0893-0.1086-0.23040.02390.0790.29420.0557-0.0740.29710.06590.4278-0.735423.951.9589
31.1483-0.69980.10481.23370.03220.8078-0.0480.14160.0704-0.029-0.0206-0.06720.0120.02990.06010.1668-0.02590.02530.41360.04950.34477.1691.8803-12.0489
41.62660.09050.57850.5806-0.04010.361-0.20140.09640.0610.02920.23880.1362-0.2047-0.35290.07280.04070.03190.00940.4787-0.00160.367-16.52467.2477-5.5398
50.6813-0.6029-0.09710.68650.02750.6364-0.05150.0744-0.12020.09380.05130.10550.05290.04160.02260.1289-0.03470.01370.33410.00280.35731.7791-10.8645-5.2792
61.1382-0.1340.62231.7765-0.49651.3987-0.2168-0.13510.01880.55330.1160.1466-0.088-0.21940.03640.33710.07220.06810.4008-0.01120.3375-6.02331.636219.9745
70.31520.20480.07071.95090.00161.8832-0.1474-0.46590.11540.76430.15720.5082-0.0944-0.12590.25891.28960.39550.09160.752-0.12310.4202-8.363816.251842.2442
81.4811-0.1940.11861.50490.59792.1505-0.17840.02940.34620.2716-0.0859-0.4048-0.28720.37390.23930.44550.0752-0.16160.26850.01220.47815.331428.59079.4101
93.32241.5903-1.09791.4866-1.62012.2973-0.6126-0.22890.39270.48820.5650.2516-0.4199-0.41950.04980.87320.3332-0.07190.5262-0.06990.4418-8.066625.496226.6879
101.0217-0.03030.16590.4131-0.38770.6505-0.5182-0.48670.99141.3360.39780.1862-0.7293-0.22880.03711.78250.5508-0.20010.7445-0.32490.4026-0.728926.329943.4854
110.44950.28530.07920.57640.40580.3593-0.46840.18990.28490.73440.0324-0.2776-0.65410.1733-0.06451.0009-0.0298-0.47560.4747-0.04830.765217.918527.136425.1176
120.36090.6048-0.10161.1058-0.02990.0623-0.3933-0.04340.60410.5884-0.3298-0.8314-0.67770.0262-1.12631.0949-0.0803-0.65660.4884-0.10591.043924.255232.03526.7618
130.4910.21830.20830.543-0.39080.5554-0.3403-0.71760.24480.6570.062-0.0155-0.3245-0.2319-0.19861.84320.3299-0.4930.6209-0.26250.40568.547317.565849.7986
140.65880.0864-0.66840.0166-0.20961.9103-0.3218-0.3512-0.05881.14520.1163-0.1108-0.15850.11120.07571.06280.294-0.07710.5188-0.01950.46944.02927.546141.0278
151.3411-0.1470.11032.1252-0.84971.3259-0.11820.01470.10240.39030.0174-0.335-0.17110.10350.21030.27680.0222-0.09970.3802-0.05230.424716.51072.961917.2021
160.66040.8772-0.18741.6804-0.08340.5875-0.1269-0.0452-0.0435-0.18530.05-0.0703-0.05210.1373-0.02690.07030.03010.02340.40250.01020.3454-11.5082-14.4782-45.6052
170.63880.74950.07981.18840.16781.1715-0.1845-0.2437-0.4003-0.2210.0201-0.36870.3135-0.00130.10370.28790.02330.12230.35060.03090.4777-16.286-33.0201-48.7743
180.76770.62230.00311.11260.06270.80150.1262-0.21090.00250.196-0.1106-0.0096-0.02880.03390.09330.13020.00070.00720.42250.01720.3516-17.5429-11.0623-35.6093
192.01550.5236-1.07421.1856-0.38541.281-0.11470.0774-0.1463-0.13060.01250.19580.2963-0.40530.00050.1711-0.0540.02030.4852-0.04680.4063-38.9224-22.0419-45.7734
200.2369-0.11010.05140.3071-0.21920.23250.2827-0.2011-0.0769-0.2097-0.28640.2910.30520.12410.02430.0489-0.01560.06150.570.00930.3627-34.3168-14.0869-36.4571
210.6370.6426-0.03521.61240.2511.219-0.0381-0.1638-0.0293-0.1281-0.0150.0884-0.3575-0.12410.06460.09370.0093-0.02580.33850.0140.353-17.93541.2648-49.2881
221.2430.7352-0.60721.9812-0.4821.5187-0.31350.0830.0233-0.64380.17950.2440.131-0.31570.07150.4122-0.0984-0.06340.3933-0.00440.3304-30.0802-15.6253-70.9668
230.2835-0.397-0.28821.4176-0.10060.7992-0.28560.6113-0.1299-0.61070.16510.51930.1829-0.3202-0.08511.6413-0.8653-0.26470.6856-0.26370.3527-32.1379-30.4498-93.2677
241.29840.46850.27711.5911-0.43531.7169-0.43850.0946-0.2778-0.63020.1795-0.35460.3346-0.120.19040.7167-0.17040.23250.4283-0.0720.5249-24.116-41.381-67.2996
250.90870.5111-0.41370.62890.18911.0049-0.85640.4092-0.8575-1.39110.338-0.1970.75740.1589-1.42651.6899-0.54750.35650.5345-0.37730.5438-20.8675-41.2236-89.903
260.54510.3274-0.22690.5185-0.30050.2062-0.2943-0.1223-0.4445-0.4948-0.0373-0.53590.35920.3417-0.85430.6590.0450.56220.4352-0.10690.8462-1.3494-36.0928-73.0366
270.93170.6135-0.2121.0870.4090.4731-0.51810.3566-0.426-1.15350.2721-0.49640.4450.0548-0.08981.4107-0.24980.52460.6507-0.10960.7278-10.9625-36.32-91.1738
282.4896-0.12660.99461.0594-0.50421.3864-0.45590.0505-0.1755-1.1830.4229-0.2652-0.0811-0.1090.18610.9653-0.21210.15880.4363-0.1050.4651-13.2905-22.2534-80.0434
291.0461-0.25020.07071.59250.0380.9626-0.1507-0.0185-0.1509-0.56830.047-0.33470.00410.14690.14950.263-0.01650.13410.3866-0.03780.4242-7.3181-15.6699-67.4988
300.4113-0.0654-0.22451.37610.11670.6209-0.01470.31560.1033-0.8801-0.084-0.1612-0.5434-0.13520.06691.2365-0.06860.03930.52860.01820.4362-15.620826.681-85.5513
310.543-0.28920.48040.6638-0.86021.2145-0.2051-0.13770.2031-0.94440.02560.1178-0.0578-0.8092-0.12661.0640.1797-0.28290.6607-0.050.5917-38.270834.4289-78.882
321.0073-0.0023-0.05721.5091-0.29490.3544-0.05850.1691-0.1273-0.64180.1180.2663-0.3445-0.20560.05650.7932-0.0079-0.05210.5157-0.00320.3519-23.870613.1724-81.1455
331.5473-0.09610.09921.9934-0.10651.146-0.0085-0.17330.0671-0.16140.03580.2893-0.4943-0.24280.04640.55040.0376-0.00720.4665-0.02810.3725-25.171826.1072-55.2272
341.43610.71380.18141.6203-0.13251.17490.1515-0.52530.38810.3961-0.14860.2493-0.5186-0.1983-0.05230.8709-0.00210.12230.6473-0.12780.5338-21.241640.3988-32.9703
350.80780.31160.24550.73850.14222.2254-0.03560.12750.4949-0.40570.1174-0.0048-0.2724-0.07810.01111.0445-0.054-0.0060.46210.08840.6201-11.152950.9729-67.5039
361.62510.6068-0.06081.4879-0.37561.11940.0293-0.3440.48850.29430.0070.0767-0.6838-0.043-0.01241.0153-0.01430.03320.5899-0.12090.5775-13.184249.4213-38.252
371.47120.3398-0.06181.8112-0.05821.0942-0.0725-0.03610.1265-0.07330.005-0.3945-0.45450.33460.0410.9577-0.21960.11510.6265-0.00540.64836.927148.1531-54.6407
381.44330.7007-0.01182.043-0.6831.41770.162-0.52820.1610.051-0.3491-0.0977-0.65970.13130.02520.7847-0.16090.00730.6496-0.08530.58811.679444.0258-35.1029
391.46510.6827-0.62811.418-0.33381.3854-0.138-0.7335-0.06990.1697-0.1535-0.2229-0.4961-0.0924-0.00850.5982-0.0968-0.00590.60570.00640.3758-11.451331.3931-33.1371
402.78290.0987-0.72980.93440.77341.0051-0.07-0.2554-0.0370.1928-0.0418-0.2632-0.5590.17030.06620.7075-0.08980.06490.4176-0.04980.3819-6.183229.5903-48.7854
411.62260.30140.30771.81480.02891.2859-0.06070.0421-0.0858-0.43330.0503-0.3178-0.46210.21340.01670.6007-0.12630.10450.4604-0.00610.459-3.510422.4426-62.2428
421.70990.02390.08070.5444-0.46291.6245-0.1422-0.12570.13260.6466-0.1006-0.40610.60160.20440.11580.88810.1099-0.17520.42790.03640.403116.265-27.935835.454
430.2887-0.1941-0.26110.6672-0.28330.46150.1582-0.1209-0.37210.43210.0535-0.36270.57560.0420.11281.2942-0.0346-0.09460.55240.14050.6079.5194-55.114227.3367
440.239-0.1612-0.0640.9629-0.16291.05770.1203-0.3142-0.08931.0385-0.21280.06940.6677-0.4733-0.08711.1967-0.1630.0640.63190.00070.4294-0.7717-39.58134.02
450.6203-0.3416-0.36410.3725-0.13971.1163-0.3233-0.3019-0.30720.977-0.0846-0.0142-0.17570.0177-0.39411.4488-0.36380.4690.76470.11140.5572-17.6086-49.994836.7111
461.07160.9103-0.12372.4124-0.75730.24910.1407-0.14180.14020.9788-0.12930.4230.6546-0.3435-0.00350.9808-0.18460.21960.5-0.01460.3854-6.6952-30.801636.0648
471.20230.3922-0.15112.63011.01241.4230.0679-0.09070.12080.7109-0.1128-0.04080.3177-0.24440.02520.62750.0131-0.04290.38590.02720.37684.7661-27.332522.791
482.0825-0.4759-0.82221.92990.28112.1128-0.0462-0.10960.0128-0.00990.11680.21330.2942-0.40560.07380.414-0.1380.06250.5138-0.01310.3762-5.7767-39.78564.3475
491.70740.0494-0.26262.06640.00281.9550.03340.1008-0.1894-0.1684-0.03520.06320.8243-0.43190.07670.5346-0.05560.00550.4258-0.02550.38812.6222-39.68721.6388
501.0398-0.21090.09251.3743-0.30291.2793-0.09010.1772-0.31050.2374-0.0436-0.02680.5614-0.0108-0.1070.8464-0.10010.00090.4351-0.00310.51177.3862-59.1103-2.3026
511.3068-0.210.23561.351-0.22621.3037-0.07810.1043-0.1908-0.0230.1004-0.23340.63490.0565-0.05280.72460.01390.01670.4162-0.09340.503619.4804-59.4771-9.4001
522.4599-0.07681.04021.00650.92751.8124-0.26430.2078-0.12380.11180.0551-0.38470.18210.2021-0.00120.44920.0786-0.04450.3585-0.07770.457117.8079-43.5557-2.1331
531.73310.061-0.1122.0979-0.01361.61450.0104-0.0369-0.01010.60460.0289-0.36710.34030.2005-0.01550.46520.0822-0.10060.3507-0.01590.385320.5014-36.440211.2593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 49 )A3 - 49
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 84 )A50 - 84
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 199 )A85 - 199
4X-RAY DIFFRACTION4chain 'A' and (resid 200 through 260 )A200 - 260
5X-RAY DIFFRACTION5chain 'A' and (resid 261 through 358 )A261 - 358
6X-RAY DIFFRACTION6chain 'A' and (resid 359 through 474 )A359 - 474
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 49 )B3 - 49
8X-RAY DIFFRACTION8chain 'B' and (resid 50 through 84 )B50 - 84
9X-RAY DIFFRACTION9chain 'B' and (resid 85 through 109 )B85 - 109
10X-RAY DIFFRACTION10chain 'B' and (resid 110 through 179 )B110 - 179
11X-RAY DIFFRACTION11chain 'B' and (resid 180 through 219 )B180 - 219
12X-RAY DIFFRACTION12chain 'B' and (resid 220 through 276 )B220 - 276
13X-RAY DIFFRACTION13chain 'B' and (resid 277 through 307 )B277 - 307
14X-RAY DIFFRACTION14chain 'B' and (resid 308 through 358 )B308 - 358
15X-RAY DIFFRACTION15chain 'B' and (resid 359 through 474 )B359 - 474
16X-RAY DIFFRACTION16chain 'C' and (resid 3 through 67 )C3 - 67
17X-RAY DIFFRACTION17chain 'C' and (resid 68 through 109 )C68 - 109
18X-RAY DIFFRACTION18chain 'C' and (resid 110 through 187 )C110 - 187
19X-RAY DIFFRACTION19chain 'C' and (resid 188 through 260 )C188 - 260
20X-RAY DIFFRACTION20chain 'C' and (resid 261 through 288 )C261 - 288
21X-RAY DIFFRACTION21chain 'C' and (resid 289 through 358 )C289 - 358
22X-RAY DIFFRACTION22chain 'C' and (resid 359 through 474 )C359 - 474
23X-RAY DIFFRACTION23chain 'D' and (resid 3 through 49 )D3 - 49
24X-RAY DIFFRACTION24chain 'D' and (resid 50 through 109 )D50 - 109
25X-RAY DIFFRACTION25chain 'D' and (resid 110 through 199 )D110 - 199
26X-RAY DIFFRACTION26chain 'D' and (resid 200 through 233 )D200 - 233
27X-RAY DIFFRACTION27chain 'D' and (resid 234 through 342 )D234 - 342
28X-RAY DIFFRACTION28chain 'D' and (resid 343 through 370 )D343 - 370
29X-RAY DIFFRACTION29chain 'D' and (resid 371 through 474 )D371 - 474
30X-RAY DIFFRACTION30chain 'E' and (resid 3 through 199 )E3 - 199
31X-RAY DIFFRACTION31chain 'E' and (resid 200 through 260 )E200 - 260
32X-RAY DIFFRACTION32chain 'E' and (resid 261 through 358 )E261 - 358
33X-RAY DIFFRACTION33chain 'E' and (resid 359 through 474 )E359 - 474
34X-RAY DIFFRACTION34chain 'F' and (resid 3 through 49 )F3 - 49
35X-RAY DIFFRACTION35chain 'F' and (resid 50 through 84 )F50 - 84
36X-RAY DIFFRACTION36chain 'F' and (resid 85 through 187 )F85 - 187
37X-RAY DIFFRACTION37chain 'F' and (resid 188 through 260 )F188 - 260
38X-RAY DIFFRACTION38chain 'F' and (resid 261 through 307 )F261 - 307
39X-RAY DIFFRACTION39chain 'F' and (resid 308 through 342 )F308 - 342
40X-RAY DIFFRACTION40chain 'F' and (resid 343 through 370 )F343 - 370
41X-RAY DIFFRACTION41chain 'F' and (resid 371 through 474 )F371 - 474
42X-RAY DIFFRACTION42chain 'G' and (resid 3 through 49 )G3 - 49
43X-RAY DIFFRACTION43chain 'G' and (resid 50 through 109 )G50 - 109
44X-RAY DIFFRACTION44chain 'G' and (resid 110 through 233 )G110 - 233
45X-RAY DIFFRACTION45chain 'G' and (resid 234 through 260 )G234 - 260
46X-RAY DIFFRACTION46chain 'G' and (resid 261 through 307 )G261 - 307
47X-RAY DIFFRACTION47chain 'G' and (resid 308 through 370 )G308 - 370
48X-RAY DIFFRACTION48chain 'G' and (resid 371 through 414 )G371 - 414
49X-RAY DIFFRACTION49chain 'G' and (resid 415 through 474 )G415 - 474
50X-RAY DIFFRACTION50chain 'H' and (resid 3 through 84 )H3 - 84
51X-RAY DIFFRACTION51chain 'H' and (resid 85 through 342 )H85 - 342
52X-RAY DIFFRACTION52chain 'H' and (resid 343 through 370 )H343 - 370
53X-RAY DIFFRACTION53chain 'H' and (resid 371 through 474 )H371 - 474

+
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