[English] 日本語
Yorodumi
- PDB-6qfb: Structure of the human ATP citrate lyase holoenzyme in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qfb
TitleStructure of the human ATP citrate lyase holoenzyme in complex with citrate, coenzyme A and Mg.ADP
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 activity / ATP citrate synthase / Fatty acyl-CoA biosynthesis / citrate metabolic process / ChREBP activates metabolic gene expression / acetyl-CoA biosynthetic process / oxaloacetate metabolic process / coenzyme A metabolic process / lipid biosynthetic process / cholesterol biosynthetic process ...ATP citrate synthase activity / ATP citrate synthase / Fatty acyl-CoA biosynthesis / citrate metabolic process / ChREBP activates metabolic gene expression / acetyl-CoA biosynthetic process / oxaloacetate metabolic process / coenzyme A metabolic process / lipid biosynthetic process / cholesterol biosynthetic process / tricarboxylic acid cycle / 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 / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
DIHYDROGENPHOSPHATE ION / ADENOSINE-5'-DIPHOSPHATE / COENZYME A / CITRATE ANION / ATP-citrate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 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
DepositionJan 9, 2019Deposition 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 1.3Jan 24, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_id

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)468,90321
Polymers463,5224
Non-polymers5,38117
Water00
1
A: ATP-citrate synthase
B: ATP-citrate synthase
hetero molecules

A: ATP-citrate synthase
B: ATP-citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)469,21324
Polymers463,5224
Non-polymers5,69120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area43640 Å2
ΔGint-284 kcal/mol
Surface area154250 Å2
MethodPISA
2
C: ATP-citrate synthase
D: ATP-citrate synthase
hetero molecules

C: ATP-citrate synthase
D: ATP-citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)468,59218
Polymers463,5224
Non-polymers5,07014
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area39800 Å2
ΔGint-263 kcal/mol
Surface area156930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)214.277, 215.398, 158.421
Angle α, β, γ (deg.)90.00, 117.27, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 4 molecules ABCD

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


Mass: 115880.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACLY / Plasmid: pET-Duet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P53396, ATP citrate synthase

-
Non-polymers , 5 types, 17 molecules

#2: Chemical ChemComp-2HP / DIHYDROGENPHOSPHATE ION


Mass: 96.987 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H2O4P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.15
Details: 17 % PEG 3350 0.2 M Na2HPO4 pH 8.15 Protein sample buffer

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.25→49.03 Å / Num. obs: 99647 / % possible obs: 99.2 % / Redundancy: 4.5 % / Biso Wilson estimate: 106.89 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.124 / Net I/σ(I): 11.11
Reflection shellResolution: 3.25→3.45 Å / Redundancy: 4.51 % / Mean I/σ(I) obs: 0.91 / Num. unique obs: 15851 / CC1/2: 0.341 / Rrim(I) all: 1.99 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3pff, 6hxi

3pff

6hxi


Resolution: 3.25→47.83 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.339
RfactorNum. reflection% reflectionSelection details
Rfree0.193 5084 5.1 %RANDOM
Rwork0.162 ---
obs0.164 99634 99.5 %-
Displacement parametersBiso mean: 137.06 Å2
Baniso -1Baniso -2Baniso -3
1-2.0732 Å20 Å212.2422 Å2
2--0.7271 Å20 Å2
3----2.8003 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: 1 / Resolution: 3.25→47.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31725 0 320 0 32045
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0132736HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1344348HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d11386SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes5555HARMONIC5
X-RAY DIFFRACTIONt_it32736HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion19.38
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4270SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance40HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact36595SEMIHARMONIC4
LS refinement shellResolution: 3.25→3.27 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2582 117 5.87 %
Rwork0.2386 1876 -
all0.2397 1993 -
obs--94.17 %
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)
15.8727-1.8971-0.93174.43211.6386.3773-0.4346-0.7986-0.11760.39120.3151-0.45380.2890.49580.1196-0.15140.28750.2793-0.0604-0.0307-0.062355.9207-197.182-18.7977
24.8913-2.05940.41955.64760.58712.3445-0.2359-0.3169-1.11670.01180.03310.15910.4153-0.24730.20280.03510.03540.4657-0.1666-0.04470.128934.5309-204.64-23.5625
32.63295.13771.633802.57630.9848-0.1303-0.08840.28280.1671-0.1783-0.29590.0469-0.13880.3086-0.15310.21140.2182-0.0106-0.10270.130347.7587-181.945-28.227
46.3424-1.84294.09064.1341-0.55795.6205-0.1920.39270.8883-0.319-0.1123-1.2435-0.1009-0.19550.3043-0.23940.25120.4712-0.04790.06880.054240.3066-162.724-43.2531
53.1754-1.8769-0.96863.5559-0.12982.19120.15790.8599-0.6042-1.0438-0.40080.10960.1449-0.26720.24290.13660.01520.05260.0865-0.368-0.442114.588-178.819-43.2197
62.4893-3.4055-2.19965.19890.3563-0.25250.23680.338-0.3161-0.50750.1067-0.09820.1835-0.1185-0.34350.13460.15960.13110.16750.2171-0.337811.4318-155.248-45.7025
71.2982-0.05330.31611.87810.21182.13870.0682-0.01080.14740.1132-0.1038-0.1796-0.22520.21030.0356-0.1471-0.0482-0.0794-0.10970.0299-0.107911.6251-143.9055.7783
81.018-0.7102-0.18174.632.65484.9099-0.0534-0.19720.42430.1120.1399-0.0588-0.60870.2032-0.08660.0751-0.1755-0.0468-0.06930.02540.091317.3168-122.87814.1089
94.10490.9693-0.83096.6684-0.33344.7773-0.0424-0.7878-0.09480.0928-0.334-0.8494-0.07370.47170.3764-0.0901-0.19240.1791-0.05460.0921-0.049335.8124-91.542344.3621
104.12721.1521-0.62659.62771.00762.1134-0.31070.07460.352-0.78570.2220.5187-0.22510.07990.08870.2203-0.07560.0755-0.2772-0.0288-0.04714.1774-85.548939.0572
114.3876-1.82991.81520-5.1540.70550.13660.1251-0.35630.0528-0.0141-0.36220.05260.0547-0.12240.0801-0.19430.08340.0075-0.20110.23824.4444-107.20347.3318
123.88360.0222-1.08454.21260.40085.7842-0.1921-0.3979-0.04540.53920.2713-0.33360.72690.9014-0.07920.08110.17190.0048-0.1946-0.1426-0.236312.0608-128.00853.0323
132.09940.98170.18713.37550.91813.2388-0.2763-0.07790.47140.0251-0.03730.7093-0.2433-0.39980.3136-0.14360.08010.0619-0.282-0.16530.0962-10.0631-112.5245.7055
14-1.10320.42232.19036.944.89885.8369-0.14530.07930.47440.40070.43150.44630.14430.2011-0.2862-0.0494-0.27280.31080.1776-0.04740.0275-15.1007-137.29144.9784
152.0145-0.03220.4381.40990.1732.0851-0.05250.11840.2315-0.0215-0.0928-0.2636-0.02480.25920.1453-0.1542-0.02150.0174-0.03950.0239-0.060312.6055-146.6671.2028
161.81420.2424-0.31343.43251.77772.80940.10340.399-0.29-0.28270.0834-0.31530.27290.271-0.1868-0.06910.0769-0.0570.1287-0.001-0.0822.4101-167.578-2.1449
173.4785-2.3077-1.08423.27562.20067.49680.1720.1546-0.98590.9056-0.2716-0.04811.617-0.04440.09960.6520.08070.0238-0.5057-0.2596-0.09092.1214-102.521117.3866
185.6512-1.44411.93836.40091.09635.37850.15520.5497-0.05050.3257-0.1533-0.54981.12190.9586-0.0019-0.05270.211-0.0051-0.0334-0.0659-0.28219.5745-80.9888120.5119
194.93852.303-3.51741.1471-7.1999-4.93850.0301-0.0491-0.23640.13510.09050.28960.1714-0.0453-0.12070.5114-0.12060.042-0.193-0.41-0.1423-12.5657-90.932118.7396
203.9738-1.1751.17428.78812.20131.65330.45120.2508-0.7736-1.0845-0.01851.5440.6487-0.758-0.43270.0668-0.3685-0.52990.1070.22560.4036-36.8035-79.8294124.1169
214.4881-1.06511.65161.9866-0.58113.5792-0.0652-0.39650.03170.3017-0.21560.1325-0.1995-0.45210.2808-0.2524-0.0497-0.041-0.0611-0.166-0.1688-18.3805-55.7976125.0857
224.3026-0.2984.15140.3386-3.06883.13670.2143-0.4858-0.15280.09920.31360.60920.26220.105-0.5279-0.08590.376-0.04990.3424-0.27430.1319-40.9093-50.5227118.7952
232.2569-0.22630.87180.79010.7571.93370.11290.20660.13320.0143-0.0038-0.12730.5944-0.0807-0.1092-0.1634-0.0199-0.2307-0.10730.00310.0877-36.952-64.464368.1856
243.1631-1.08192.69652.01340.1066.58350.33380.08450.0758-0.43050.01310.23610.9-0.6389-0.3469-0.0174-0.2723-0.3275-0.04920.12570.0504-55.2919-72.507955.7547
256.32640.9321.84665.43520.68867.3789-0.27030.04041.056-0.1354-0.00750.1814-1.24610.18050.27770.59960.3246-0.0467-0.5414-0.1662-0.0863-95.6851-3.276890.3718
267.8084-1.42110.95946.0739-0.14823.7058-0.1067-0.1609-0.061-0.4316-0.03690.6385-0.7567-0.59040.14360.10680.30940.0659-0.2263-0.108-0.2378-102.645-25.129687.4546
27-1.50296.35261.043.7161-0.15591.621-0.2142-0.00750.3862-0.12480.2019-0.2517-0.10940.01720.01230.0770.31380.132-0.4687-0.0280.4987-82.8158-14.1046100.6732
285.02890.0589-0.376510.7053-3.45882.5087-0.3535-0.10281.0877-0.0327-0.2272-1.13690.05810.25290.5807-0.03040.3782-0.0688-0.3428-0.26840.0419-66.9622-25.4078117.2528
293.8303-1.1287-0.12051.98650.41412.4282-0.1632-0.756-0.12810.6340.18380.291-0.1503-0.1823-0.0206-0.03780.04080.0667-0.27240.06240.0248-80.6377-49.7288105.8934
305.988-3.9935-1.724902.40094.98140.0587-0.4010.0840.26380.5121-0.11120.27390.1779-0.5708-0.07920.3388-0.2386-0.09510.056-0.0624-57.8593-53.7164113.4184
312.4961-0.1652-0.48921.44520.42163.60470.06610.04670.7126-0.03130.07880.1909-0.55940.1412-0.1448-0.3686-0.0155-0.1481-0.20050.02730.3128-33.9403-39.486168.0918
325.5458-0.1552-1.49661.9371-0.94142.84550.508-0.07741.0956-0.2484-0.1934-0.453-0.50060.4859-0.3146-0.2711-0.2082-0.0196-0.2565-0.08790.5201-12.3028-30.295368.1815
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|26 - A|115 }
2X-RAY DIFFRACTION2{ A|2 - A|25 A|116 - A|235 }
3X-RAY DIFFRACTION3{ A|236 - A|248 }
4X-RAY DIFFRACTION4{ A|249 - A|425 }
5X-RAY DIFFRACTION5{ A|488 - A|807 }
6X-RAY DIFFRACTION6{ A|808 - A|837 }
7X-RAY DIFFRACTION7{ A|838 - A|936 A|1055 - A|1097 }
8X-RAY DIFFRACTION8{ A|937 - A|1054 }
9X-RAY DIFFRACTION9{ B|26 - B|115 }
10X-RAY DIFFRACTION10{ B|2 - B|25 B|116 - B|235 }
11X-RAY DIFFRACTION11{ B|236 - B|248 }
12X-RAY DIFFRACTION12{ B|249 - B|425 }
13X-RAY DIFFRACTION13{ B|488 - B|807 }
14X-RAY DIFFRACTION14{ B|808 - B|837 }
15X-RAY DIFFRACTION15{ B|838 - B|936 B|1055 - B|1098 }
16X-RAY DIFFRACTION16{ B|937 - B|1054 }
17X-RAY DIFFRACTION17{ C|26 - C|115 }
18X-RAY DIFFRACTION18{ C|2 - C|25 C|116 - C|235 }
19X-RAY DIFFRACTION19{ C|236 - C|248 }
20X-RAY DIFFRACTION20{ C|249 - C|421 }
21X-RAY DIFFRACTION21{ C|488 - C|807 }
22X-RAY DIFFRACTION22{ C|808 - C|837 }
23X-RAY DIFFRACTION23{ C|838 - C|936 C|1055 - C|1095 }
24X-RAY DIFFRACTION24{ C|937 - C|1054 }
25X-RAY DIFFRACTION25{ D|26 - D|115 }
26X-RAY DIFFRACTION26{ D|2 - D|25 D|116 - D|235 }
27X-RAY DIFFRACTION27{ D|236 - D|248 }
28X-RAY DIFFRACTION28{ D|249 - D|425 }
29X-RAY DIFFRACTION29{ D|488 - D|807 }
30X-RAY DIFFRACTION30{ D|808 - D|837 }
31X-RAY DIFFRACTION31{ D|838 - D|936 D|1055 - D|1101 }
32X-RAY DIFFRACTION32{ D|937 - D|1054 }

+
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://pdbjlvh1.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