[English] 日本語
Yorodumi
- PDB-6hxl: Structure of the citryl-CoA lyase core module of human ATP citrat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hxl
TitleStructure of the citryl-CoA lyase core module of human ATP citrate lyase in complex with citrate and CoASH (space group P21)
ComponentsATP-citrate synthase
KeywordsLYASE / ATP citrate lyase / central metabolism / acetyl-Coa / citrate shuttle / rTCA cycle / citryl-CoA / lipogenesis
Function / homology
Function and homology information


ATP citrate synthase / ATP citrate synthase activity / citrate metabolic process / Fatty acyl-CoA biosynthesis / ChREBP activates metabolic gene expression / acetyl-CoA biosynthetic process / coenzyme A metabolic process / oxaloacetate metabolic process / lipid biosynthetic process / cholesterol biosynthetic process ...ATP citrate synthase / ATP citrate synthase activity / citrate metabolic process / Fatty acyl-CoA biosynthesis / ChREBP activates metabolic gene expression / acetyl-CoA biosynthetic process / coenzyme A metabolic process / oxaloacetate metabolic process / lipid biosynthetic process / cholesterol biosynthetic process / fatty acid biosynthetic process / azurophil granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / metal ion binding / cytosol
Similarity search - Function
ATP-citrate synthase / ATP-citrate synthase, citrate-binding domain / ATP citrate lyase citrate-binding / ATP-citrate lyase/succinyl-CoA ligase, active site / ATP-citrate lyase/succinyl-CoA ligase, conserved site / ATP-citrate lyase / succinyl-CoA ligases family active site. / ATP-citrate lyase / succinyl-CoA ligases family signature 1. / Succinyl-CoA synthetase, beta subunit, conserved site / ATP-citrate lyase / succinyl-CoA ligases family signature 3. / ATP-citrate lyase/succinyl-CoA ligase ...ATP-citrate synthase / ATP-citrate synthase, citrate-binding domain / ATP citrate lyase citrate-binding / ATP-citrate lyase/succinyl-CoA ligase, active site / ATP-citrate lyase/succinyl-CoA ligase, conserved site / ATP-citrate lyase / succinyl-CoA ligases family active site. / ATP-citrate lyase / succinyl-CoA ligases family signature 1. / Succinyl-CoA synthetase, beta subunit, conserved site / ATP-citrate lyase / succinyl-CoA ligases family signature 3. / ATP-citrate lyase/succinyl-CoA ligase / CoA-ligase / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Citrate synthase / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
OXIDIZED COENZYME A / COENZYME A / CITRATE ANION / DI(HYDROXYETHYL)ETHER / ATP-citrate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsVerstraete, K. / Verschueren, K.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders1524918N Belgium
CitationJournal: Nature / Year: 2019
Title: Structure of ATP citrate lyase and the origin of citrate synthase in the Krebs cycle.
Authors: Verschueren, K.H.G. / Blanchet, C. / Felix, J. / Dansercoer, A. / De Vos, D. / Bloch, Y. / Van Beeumen, J. / Svergun, D. / Gutsche, I. / Savvides, S.N. / Verstraete, K.
History
DepositionOct 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 8, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 1, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-citrate synthase
B: ATP-citrate synthase
C: ATP-citrate synthase
D: ATP-citrate synthase
E: ATP-citrate synthase
F: ATP-citrate synthase
G: ATP-citrate synthase
H: ATP-citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,63226
Polymers240,0648
Non-polymers7,56818
Water30,8601713
1
A: ATP-citrate synthase
B: ATP-citrate synthase
C: ATP-citrate synthase
D: ATP-citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,96814
Polymers120,0324
Non-polymers3,93610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27360 Å2
ΔGint-196 kcal/mol
Surface area36560 Å2
MethodPISA
2
E: ATP-citrate synthase
F: ATP-citrate synthase
G: ATP-citrate synthase
H: ATP-citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,66512
Polymers120,0324
Non-polymers3,6338
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27060 Å2
ΔGint-174 kcal/mol
Surface area37400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.711, 147.895, 113.688
Angle α, β, γ (deg.)90.00, 105.28, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
ATP-citrate synthase / ATP-citrate (pro-S-)-lyase / ACL / Citrate cleavage enzyme


Mass: 30008.025 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Before crystallization, the N-terminal sequence MGSSHHHHHHSSGLVPR was removed by thrombin digestion.
Source: (gene. exp.) Homo sapiens (human) / Gene: ACLY / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P53396, ATP citrate synthase

-
Non-polymers , 7 types, 1731 molecules

#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CAO / OXIDIZED COENZYME A


Mass: 783.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1713 / 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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 21% PEG8000 0.1 M HEPES pH 7.0 0.15 M ammonium sulphate Protein sample buffer 20 mM HBS, 150 mM NaCl, pH 7.4 supplemented with 50 mM citrate pH 7.4 and 10 mM CoASH

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 458935 / % possible obs: 97.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.9 % / Biso Wilson estimate: 13 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.072 / Rrim(I) all: 0.128 / Net I/av σ(I): 8.96 / Net I/σ(I): 8.96
Reflection shellResolution: 1.35→1.43 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.641 / Mean I/σ(I) obs: 1.05 / Num. unique obs: 71629 / CC1/2: 0.421 / Rpim(I) all: 1.041 / Rrim(I) all: 1.645 / % possible all: 94.2

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: M. soehngenii ACL structure

Resolution: 1.35→47.85 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.048 / SU Rfree Blow DPI: 0.049 / SU Rfree Cruickshank DPI: 0.048
RfactorNum. reflection% reflectionSelection details
Rfree0.174 23064 5.03 %RANDOM
Rwork0.156 ---
obs0.157 458802 97.5 %-
Displacement parametersBiso mean: 20.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.622 Å20 Å20.0602 Å2
2---1.4075 Å20 Å2
3---0.7855 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: 1 / Resolution: 1.35→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16312 0 478 1713 18503
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0134997HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1163490HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7874SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes364HARMONIC2
X-RAY DIFFRACTIONt_gen_planes5122HARMONIC5
X-RAY DIFFRACTIONt_it34997HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.89
X-RAY DIFFRACTIONt_other_torsion14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2248SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies104HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact41414SEMIHARMONIC4
LS refinement shellResolution: 1.35→1.39 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 1666 5.18 %
Rwork0.226 30527 -
all0.226 32193 -
obs--92.65 %
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)
11.03360.66810.43352.68291.07522.0811-0.04610.15710.1568-0.20760.02120.0024-0.06470.09790.0249-0.02970.00660.0022-0.00470.0615-0.021520.478221.2801-70.2809
20.86270.2557-0.3060.68390.04822.95310.02470.14290.1894-0.0220.06360.0817-0.1783-0.0888-0.0883-0.04480.01870.0084-0.04510.04690.015214.710824.3888-56.4071
30.4199-0.25970.02170.5856-0.04910.26520.00470.02210.01230.0291-0.01230.06450.0131-0.05330.0076-0.0445-0.00180.0039-0.04560.0018-0.033314.84826.0953-45.6115
46.1572-0.11610.5730.00290.1517-0.14640.2052-0.4951-0.39840.0443-0.07930.26450.2417-0.4137-0.1259-0.0047-0.0533-0.01540.07380.03130.0932-12.004113.2697-40.2862
50.393-0.2326-0.29421.4513-0.04020.33860.0117-0.035-0.0339-0.05450.04470.18170.0661-0.0156-0.0564-0.0118-0.02970.0036-0.0209-0.0083-0.02023.660411.56-35.2189
60.3272-0.29720.69331.6252-1.32221.58650.0116-0.14280.23070.14010.03430.0397-0.198-0.1361-0.0459-0.0240.03280.0229-0.0452-0.00260.01628.031727.7101-42.2617
72.2403-0.46880.47661.0604-0.04212.640.1035-0.13050.15430.0229-0.07580.0866-0.0038-0.1719-0.0277-0.052-0.01490.012-0.0383-0.015100.400119.1498-41.3798
81.6954-0.9993-0.83971.28640.88695.88420.07770.41280.0489-0.1471-0.02940.0071-0.3559-0.306-0.0482-0.09370.0431-0.01760.09270.0634-0.00611.571419.7276-60.7562
91.6715-0.5890.56981.0462-0.1750.87750.03520.01070.07750.0677-0.0347-0.0871-0.00960.0448-0.0005-0.04960.00810.0027-0.05210.0059-0.042223.332410.2933-46.1783
103.42851.4002-1.31521.2818-0.95960.5790.0638-0.1506-0.00790.2135-0.0406-0.05340.00520.046-0.02320.0247-0.00960.0073-0.01220.0057-0.038221.5396-11.9535-33.6399
110.6195-0.27020.62980.6864-0.25761.62240.06270.1505-0.1024-0.2242-0.07650.02760.14-0.030.01380.01550.026300.0012-0.0515-0.057118.9024-21.5676-74.2467
120.12830.0761-0.06411.2095-0.04732.4092-0.00920.0693-0.0694-0.14260.047-0.1040.1731-0.0175-0.0378-0.02160.00240.0098-0.0318-0.02390.007525.4501-27.5092-60.8121
130.4283-0.2213-0.02310.544900.16040.00830.0189-0.00790.0396-0.0246-0.0352-0.010.0220.0163-0.0295-0.0014-0.0038-0.02480.0048-0.027225.7274-11.1499-47.4469
146.1771-1.0703-0.79710.1571-1.2570.78150.0654-0.44850.60860.0118-0.1804-0.3331-0.27360.56440.115-0.0622-0.0747-0.02130.07960.01520.125852.7142-19.4019-43.6134
152.21710.3497-0.3643.05720.66071.47510.0423-0.0687-0.02030.0970.0336-0.2249-0.09180.0636-0.076-0.053-0.0124-0.0437-0.06580.0205-0.047637.3637-17.9626-38.5202
160.72190.1385-0.41471.14631.10352.6454-0.0184-0.0024-0.22380.0660.0754-0.08290.22490.1259-0.057-0.04080.0179-0.0153-0.0573-0.01010.025231.9881-32.792-47.9696
171.2003-0.3831-0.53650.759-0.28691.769-0.0061-0.079-0.1632-0.0046-0.0105-0.1179-0.04410.16470.0166-0.0467-0.0087-0.0118-0.02390.01120.016439.8661-24.7592-45.8222
180.5173-3.09533.61410.6819-2.23592.2125-0.0010.32840.0035-0.63580.1737-0.05130.1250.2846-0.17280.0135-0.05560.14110.0264-0.0720.021338.6865-22.1317-64.4241
191.6563-0.1579-0.31580.86140.14710.6770.03330.0644-0.06330.06-0.04880.07430.0064-0.08190.0155-0.02180.0029-0.001-0.02640.0039-0.015317.7915-15.2873-48.9949
201.27630.88880.37481.29651.03750.9860.0246-0.14370.01570.1863-0.07560.05310.031-0.04540.0510.0275-0.004-0.005-0.01360.0123-0.020718.46723.4875-32.3402
210.86650.33560.4051.58620.37661.34010.0383-0.0721-0.19070.1495-0.00690.08060.03230.0125-0.0314-0.0187-0.00930.0162-0.04780.0303-0.031316.6099-23.5283-37.7421
220.5426-0.12460.49811.2277-0.34091.31290.0272-0.0359-0.08760.01590.07170.13850.0778-0.0599-0.0989-0.0447-0.0078-0.0037-0.02960.01030.01519.686-26.5311-52.3263
230.46980.13770.03070.4575-0.10010.2444-0.00020.05940.0044-0.04130.01050.05830.0073-0.0355-0.0104-0.02060.01240.0003-0.00690.0012-0.023212.7119-8.5813-62.6379
240.9264-1.99152.701301.91411.4153-0.0090.13670.54530.01290.1487-0.0469-0.0427-0.5655-0.1397-0.09610.0490.02830.03050.08510.1598-14.8371-10.1127-67.2273
250.38320.95680.12021.3134-0.37851.22990.01770.15940.09610.01780.08940.2151-0.0919-0.1091-0.1071-0.0380.0212-0.0157-0.01240.0136-0.0320.4418-11.0357-72.5725
261.6790.7837-0.84142.7191-2.01661.90630.07290.1359-0.2347-0.14420.04010.12220.1495-0.0821-0.1129-0.0437-0.0137-0.0482-0.0592-0.029-0.00422.4263-28.0025-65.9206
272.38070.5686-1.08141.1832-0.95912.37310.01650.2171-0.1028-0.09390.03060.06450.0449-0.1963-0.0472-0.03880.0112-0.0173-0.0134-0.0139-0.0065-3.6426-18.547-66.0758
281.59750.4252-0.37680.7213-0.41510.5780.0676-0.0655-0.0436-0.045-0.03450.06590.00210.0091-0.0331-0.04470.0002-0.0079-0.0245-0.0093-0.024912.212-16.1072-56.9088
291.6717-1.20240.46172.2899-0.84850.1540.02910.11910.0515-0.2435-0.0352-0.08-0.02370.04880.00610.02150.00890.01780.02220.0255-0.055722.73367.819-75.2061
300.53470.1345-0.40840.89740.01251.32290.0185-0.07420.15510.11420.0183-0.0615-0.0427-0.0184-0.0368-0.0357-0.0086-0.0042-0.0573-0.0227-0.030523.58818.0356-34.7095
310.6132-0.37820.48021.2642-0.95942.8577-0.0480.0060.09950.1551-0.0247-0.111-0.22470.12720.0727-0.0425-0.017-0.0074-0.04720.01390.00430.47222.46-48.0048
320.3715-0.00220.16450.4992-0.13110.3555-0.00090.06620.022-0.0462-0.0439-0.06730.02450.08150.0448-0.03920.01690.0149-0.01560.0183-0.038127.04866.6807-61.6466
335.3262-3.0382.56462.5218-2.3122.02380.0892-0.2765-0.2849-0.0858-0.2617-0.33670.24920.5680.1725-0.25310.09080.10550.10430.43220.373756.349911.9174-64.8311
340.9011.9733-1.37634.1593-2.56553.6371-0.0692-0.0803-0.2165-0.15-0.1365-0.2240.12280.24380.2057-0.11330.03980.0521-0.03420.062-0.073241.638615.4484-71.7786
353.2913-0.12661.53661.76810.34313.89090.090.20830.3257-0.0143-0.1597-0.2513-0.210.16210.0697-0.0962-0.02720.0246-0.04980.08660.02237.652927.6811-60.6141
360.7713-0.1878-0.09040.8001-0.22532.55570.06940.13110.2625-0.0686-0.2547-0.28680.00150.31420.1854-0.08760.03220.03410.04330.13070.03944.68619.2399-63.4644
372.23610.2496-0.51921.76890.061.25490.0053-0.09120.08170.0297-0.06440.003-0.02790.26860.0592-0.0589-0.0035-0.02430.03760.04430.018442.122814.4161-44.811
381.3533-0.05740.23171.20260.23090.89480.02250.0070.1145-0.0817-0.06090.0246-0.0218-0.04280.0384-0.02860.01350.0108-0.02240.0239-0.026219.890811.9427-60.2985
392.5621-1.946-0.3793.16281.47762.25920.02120.1317-0.0308-0.2351-0.00320.05380.03360.0988-0.0180.01540.01370.00150.02130.003-0.063817.1886-7.5459-76.5788
400.6136-0.27750.61170.8714-0.12312.4297-0.02570.0832-0.1696-0.08870.1219-0.04240.0421-0.051-0.0962-0.02590.00190.0127-0.0506-0.0335-0.00616.19815.1904-14.3882
410.63070.31930.20360.6505-0.63753.30050.01280.1118-0.1297-0.04110.0896-0.03460.23770.0951-0.1024-0.03180.02830.0073-0.0618-0.02750.013322.468511.6569-0.9949
420.0252-0.1864-0.09150.59130.17240.3328-0.0222-0.0174-0.00610.01330.021-0.0911-0.01310.06830.0012-0.04670.00530.0084-0.04360.0014-0.00522.802129.251110.4659
432.5534-1.77910.25040.00080.9757-0.05370.0996-0.64240.3602-0.1293-0.0861-0.2101-0.01990.3571-0.0135-0.0964-0.07980.0490.2442-0.04490.096149.559822.346715.3501
442.596-0.6329-1.09683.12820.4034-0.0323-0.1014-0.36660.0407-0.0550.2301-0.348-0.0930.2342-0.1287-0.0706-0.0180.00880.0528-0.0363-0.020933.235423.426720.8615
450.3673-0.2367-0.79291.81161.01480.8839-0.0434-0.3337-0.18110.17540.0493-0.0570.13190.2321-0.0058-0.08990.05750.0082-0.05310.02120.025628.82937.873412.7641
464.4508-0.9118-1.13551.53160.32992.85130.0457-0.6628-0.1395-0.0038-0.0920.057-0.10960.22150.0463-0.1342-0.02630.01760.00910.0028-0.02836.606815.836813.7053
474.0435-0.690.88260.0286-1.95031.75660.04730.33880.13-0.19070.03130.05970.29160.2883-0.0786-0.06520.0469-0.0110.0799-0.04720.057135.57616.5714-5.1619
481.0992-0.2962-0.34650.8750.22321.4643-0.0201-0.0097-0.04750.030.01030.02280.0807-0.01390.0098-0.0480.01370.009-0.0610.0056-0.023514.057225.37879.9182
494.52432.02571.74071.4261.43470.61340.1965-0.3779-0.01330.3005-0.1330.04770.0656-0.078-0.06360.0273-0.0084-0.01960.0309-0.0058-0.012216.776847.178623.5578
500.5089-0.00960.0721.23980.53222.0042-0.051-0.1124-0.17260.02580.03760.04120.1010.10690.0134-0.03580.01280.0231-0.0370.0411-0.006213.599616.775820.9104
510.16450.2834-0.50672.30630.7851.9641-0.0506-0.0568-0.05940.07750.03380.07470.1685-0.03990.0168-0.01520.00410.0086-0.03430.00650.00617.007215.234912.0878
522.06431.6592-2.15522.8035-1.16264.3577-0.0162-0.00950.00210.04390.01150.09940.1886-0.11620.0047-0.0364-0.01010.0037-0.04630.00590.01836.632311.29331.7725
530.2690.0444-0.04470.54660.18190.6038-0.02460.0244-0.022-0.054-0.00220.0971-0.0947-0.15240.0268-0.02890.0298-0.0033-0.01610.0009-0.0131.972528.6282-6.807
540.65820.5602-0.94921.0913-1.28113.15010.04510.1167-0.0995-0.0232-0.05010.0388-0.0111-0.13260.005-0.0559-0.0140.005-0.0163-0.0046-0.0196-0.109811.9763-10.5717
551.38010.2282-1.07170.78180.05213.30860.01370.2806-0.1042-0.0768-0.12730.1369-0.0778-0.45660.1136-0.0780.0276-0.00870.0454-0.04030.0009-7.0817.271-7.5277
561.73390.26520.04531.35260.36551.28540.0009-0.1154-0.00970.0419-0.0256-0.02740.0149-0.23020.0247-0.06480.00810.01740.0076-0.00750.0001-4.836721.205410.9584
570.54070.426-0.2711.4208-0.43650.841-0.09810.0493-0.0474-0.2030.0852-0.0239-0.02190.06220.013-0.0068-0.0267-0.0006-0.0509-0.0219-0.060518.144334.0032-11.4207
580.58710.0051-0.81140.6861-1.16092.133-0.09630.11370.0952-0.26170.1608-0.01640.1074-0.0751-0.06460.0101-0.0142-0.0083-0.05160.0193-0.02718.188259.1559-16.0611
590.70650.06020.08380.75850.86812.67640.01360.04210.0136-0.05930.0837-0.0261-0.1676-0.0579-0.0973-0.03750.0116-0.0099-0.07750.0111-0.015911.972463.7484-2.765
600.0993-0.01930.08530.4057-0.2080.3031-0.0273-0.02390.01860.01090.02320.02990.0032-0.05860.0041-0.01860.0075-0.0051-0.0195-0.0048-0.00212.008546.5189.9482
612.5332-0.80441.30710.5287-0.26991.43260.0628-0.1848-0.1922-0.01040.04760.19790.1449-0.2016-0.1105-0.0386-0.00710.0122-0.00680.02620.0099-6.449453.89516.7733
62-0.3602-0.49482.32840.9589-2.12243.2773-0.0902-0.1991-0.02070.14550.13060.0965-0.2167-0.305-0.0405-0.03490.06450.01680.00420.0211-0.00845.474768.464710.0663
630.8533-0.9450.10291.2429-0.33451.7471-0.003-0.07650.07980.03210.0028-0.01240.0534-0.06280.0002-0.0395-0.00860.0057-0.00840.0210.0089-2.380560.421211.8391
642.4885-2.0852-0.58480.00131.0242.82170.17950.1383-0.1473-0.17310.0640.058-0.2077-0.2398-0.2436-0.04970.0254-0.00230.00720.04340.0858-1.270458.2747-6.94
651.0418-0.0020.48290.61180.04511.2513-0.0337-0.0050.08080.0154-0.0095-0.0598-0.05770.02980.0432-0.0350.01-0.0068-0.0511-0.0079-0.01520.605650.87988.6845
661.70780.8116-1.02150.5538-1.02970.18330.1076-0.2384-0.00130.2065-0.0948-0.0678-0.06720.0507-0.01280.0365-0.01680.00760.02980.0010.008819.097331.373323.845
670.51760.2376-0.66181.1338-0.44051.8696-0.014-0.14080.12880.08510.03260.0093-0.0888-0.0489-0.0186-0.02360.0009-0.0226-0.0308-0.0375-0.004320.797860.222719.0026
680.63570.0976-0.04741.5424-0.32791.95250.0019-0.04370.11110.0515-0.0129-0.0744-0.13980.0820.011-0.0276-0.0021-0.0096-0.0425-0.01540.003527.329661.03910.2338
691.15351.42571.38942.00120.97233.05370.01150.0022-0.0126-0.04690.0355-0.139-0.16650.0803-0.0469-0.0139-0.01090-0.042-0.01290.024827.619764.2289-0.4855
700.3120.41670.19580.6070.12440.4203-0.09480.0282-0.0369-0.08270.0708-0.06040.02920.08590.024-0.01230.0010.0033-0.0434-0.0101-0.027224.238545.22-6.0749
712.25790.14682.84121.1427-0.93243.9340.21560.564-0.2444-0.1728-0.1478-0.11880.31670.7368-0.0677-0.06240.12220.00250.1552-0.0621-0.043345.710451.7222-14.186
722.3936-0.14010.55831.08460.6462.03690.1370.20680.1071-0.0487-0.0442-0.1842-0.01950.0541-0.0928-0.0732-0.0212-0.0006-0.06690.0067-0.005434.656566.1826-7.6603
732.1053-0.29071.06290.63990.06872.03320.11330.44640.052-0.131-0.1472-0.02830.07430.40750.0339-0.04560.0318-0.00150.06820.0087-0.023841.716557.8964-9.08
741.67950.53170.86430.81930.19041.07170.0002-0.05250.0188-0.09130.0026-0.00710.01810.0185-0.0028-0.04410.0032-0.0011-0.0656-0.0034-0.035125.723852.31220.5633
751.7994-2.2125-0.44213.48661.63860.68080.04260.1337-0.056-0.3031-0.06440.0607-0.0735-0.0120.02180.0298-0.01520.0245-0.032-0.0106-0.020814.29629.2382-18.818
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|837 - A|867 }
2X-RAY DIFFRACTION2{ A|868 - A|896 }
3X-RAY DIFFRACTION3{ A|897 - A|952 }
4X-RAY DIFFRACTION4{ A|953 - A|965 }
5X-RAY DIFFRACTION5{ A|966 - A|984 }
6X-RAY DIFFRACTION6{ A|985 - A|1001 }
7X-RAY DIFFRACTION7{ A|1002 - A|1039 }
8X-RAY DIFFRACTION8{ A|1040 - A|1055 }
9X-RAY DIFFRACTION9{ A|1056 - A|1079 }
10X-RAY DIFFRACTION10{ A|1080 - A|1097 }
11X-RAY DIFFRACTION11{ B|837 - B|867 }
12X-RAY DIFFRACTION12{ B|868 - B|896 }
13X-RAY DIFFRACTION13{ B|897 - B|952 }
14X-RAY DIFFRACTION14{ B|953 - B|965 }
15X-RAY DIFFRACTION15{ B|966 - B|984 }
16X-RAY DIFFRACTION16{ B|985 - B|1001 }
17X-RAY DIFFRACTION17{ B|1002 - B|1039 }
18X-RAY DIFFRACTION18{ B|1040 - B|1055 }
19X-RAY DIFFRACTION19{ B|1056 - B|1078 }
20X-RAY DIFFRACTION20{ B|1079 - B|1097 }
21X-RAY DIFFRACTION21{ C|836 - C|867 }
22X-RAY DIFFRACTION22{ C|868 - C|896 }
23X-RAY DIFFRACTION23{ C|897 - C|952 }
24X-RAY DIFFRACTION24{ C|953 - C|965 }
25X-RAY DIFFRACTION25{ C|966 - C|984 }
26X-RAY DIFFRACTION26{ C|985 - C|1001 }
27X-RAY DIFFRACTION27{ C|1002 - C|1039 }
28X-RAY DIFFRACTION28{ C|1040 - C|1078 }
29X-RAY DIFFRACTION29{ C|1080 - C|1097 }
30X-RAY DIFFRACTION30{ D|837 - D|867 }
31X-RAY DIFFRACTION31{ D|868 - D|896 }
32X-RAY DIFFRACTION32{ D|897 - D|951 }
33X-RAY DIFFRACTION33{ D|952 - D|965 }
34X-RAY DIFFRACTION34{ D|966 - D|984 }
35X-RAY DIFFRACTION35{ D|985 - D|1001 }
36X-RAY DIFFRACTION36{ D|1002 - D|1039 }
37X-RAY DIFFRACTION37{ D|1040 - D|1055 }
38X-RAY DIFFRACTION38{ D|1056 - D|1079 }
39X-RAY DIFFRACTION39{ D|1080 - D|1097 }
40X-RAY DIFFRACTION40{ E|837 - E|867 }
41X-RAY DIFFRACTION41{ E|868 - E|896 }
42X-RAY DIFFRACTION42{ E|897 - E|952 }
43X-RAY DIFFRACTION43{ E|953 - E|966 }
44X-RAY DIFFRACTION44{ E|967 - E|984 }
45X-RAY DIFFRACTION45{ E|985 - E|1001 }
46X-RAY DIFFRACTION46{ E|1002 - E|1039 }
47X-RAY DIFFRACTION47{ E|1040 - E|1055 }
48X-RAY DIFFRACTION48{ E|1056 - E|1079 }
49X-RAY DIFFRACTION49{ E|1080 - E|1097 }
50X-RAY DIFFRACTION50{ F|837 - F|867 }
51X-RAY DIFFRACTION51{ F|868 - F|883 }
52X-RAY DIFFRACTION52{ F|884 - F|896 }
53X-RAY DIFFRACTION53{ F|897 - F|974 }
54X-RAY DIFFRACTION54{ F|975 - F|1001 }
55X-RAY DIFFRACTION55{ F|1002 - F|1039 }
56X-RAY DIFFRACTION56{ F|1040 - F|1055 }
57X-RAY DIFFRACTION57{ F|1056 - F|1096 }
58X-RAY DIFFRACTION58{ G|836 - G|867 }
59X-RAY DIFFRACTION59{ G|868 - G|896 }
60X-RAY DIFFRACTION60{ G|897 - G|951 }
61X-RAY DIFFRACTION61{ G|952 - G|984 }
62X-RAY DIFFRACTION62{ G|985 - G|1001 }
63X-RAY DIFFRACTION63{ G|1002 - G|1039 }
64X-RAY DIFFRACTION64{ G|1040 - G|1055 }
65X-RAY DIFFRACTION65{ G|1056 - G|1078 }
66X-RAY DIFFRACTION66{ G|1079 - G|1097 }
67X-RAY DIFFRACTION67{ H|837 - H|867 }
68X-RAY DIFFRACTION68{ H|868 - H|883 }
69X-RAY DIFFRACTION69{ H|884 - H|896 }
70X-RAY DIFFRACTION70{ H|897 - H|951 }
71X-RAY DIFFRACTION71{ H|952 - H|984 }
72X-RAY DIFFRACTION72{ H|985 - H|1001 }
73X-RAY DIFFRACTION73{ H|1002 - H|1039 }
74X-RAY DIFFRACTION74{ H|1040 - H|1078 }
75X-RAY DIFFRACTION75{ H|1079 - H|1098 }

+
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