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- PDB-2vze: Crystal structure of human acyl-CoA synthetase medium-chain famil... -

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Basic information

Entry
Database: PDB / ID: 2vze
TitleCrystal structure of human acyl-CoA synthetase medium-chain family member 2A (L64P mutation) in complex with AMP
ComponentsACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL
KeywordsLIGASE / METAL-BINDING / TRANSIT PEPTIDE / LIPID METABOLISM / NUCLEOTIDE-BINDING / ATP-BINDING / ADENYLATE-FORMING ENZYME / FATTY ACID METABOLISM / FATTY ACID-COA LIGASE
Function / homology
Function and homology information


Conjugation of salicylate with glycine / fatty acid ligase activity / decanoate-CoA ligase activity / medium-chain acyl-CoA ligase / : / benzoate-CoA ligase / benzoate-CoA ligase activity / medium-chain fatty-acyl-CoA metabolic process / acyl-CoA metabolic process / fatty-acyl-CoA synthase activity ...Conjugation of salicylate with glycine / fatty acid ligase activity / decanoate-CoA ligase activity / medium-chain acyl-CoA ligase / : / benzoate-CoA ligase / benzoate-CoA ligase activity / medium-chain fatty-acyl-CoA metabolic process / acyl-CoA metabolic process / fatty-acyl-CoA synthase activity / triglyceride homeostasis / Aspirin ADME / fatty acid biosynthetic process / glucose homeostasis / mitochondrial matrix / mitochondrion / ATP binding / metal ion binding
Similarity search - Function
ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily ...ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Acyl-coenzyme A synthetase ACSM2A, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsYue, W.W. / Kochan, G.T. / Pilka, E.S. / Bhatia, C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Wikstrom, M. / Bountra, C. / Oppermann, U.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural Snapshots for the Conformation- Dependent Catalysis by Human Medium-Chain Acyl- Coenzyme a Synthetase Acsm2A.
Authors: Kochan, G. / Pilka, E.S. / Delft, F.V. / Oppermann, U. / Yue, W.W.
History
DepositionJul 31, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Mar 27, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / struct_biol
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL
B: ACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL
C: ACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,0707
Polymers190,0043
Non-polymers1,0664
Water11,800655
1
A: ACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6822
Polymers63,3351
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6822
Polymers63,3351
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7063
Polymers63,3351
Non-polymers3722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.730, 97.730, 384.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11C-2146-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C
13A
23B
14A
24B
34C
15A
25B
35C

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISLEULEU3AA37 - 28830 - 281
21HISHISLEULEU3BB37 - 28830 - 281
31GLYGLYLEULEU3CC36 - 28829 - 281
12HISHISTHRTHR3AA330 - 385323 - 378
22HISHISTHRTHR3BB330 - 385323 - 378
32HISHISTHRTHR3CC330 - 385323 - 378
13TYRTYRLEULEU4AA390 - 511383 - 504
23TYRTYRLEULEU4BB390 - 511383 - 504
14HISHISLEULEU4AA530 - 548523 - 541
24HISHISLEULEU4BB530 - 548523 - 541
34HISHISLEULEU4CC530 - 548523 - 541
15ASPASPGLNGLN3AA292 - 321285 - 314
25ASPASPGLNGLN3BB292 - 321285 - 314
35ASPASPGLNGLN3CC292 - 321285 - 314

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein ACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL / ACYL-COA SYNTHETASE MEDIUM-CHAIN FAMILY MEMBER 2A / MIDDLE-CHAIN ACYL-COA SYNTHETASE 2A / BUTYRYL ...ACYL-COA SYNTHETASE MEDIUM-CHAIN FAMILY MEMBER 2A / MIDDLE-CHAIN ACYL-COA SYNTHETASE 2A / BUTYRYL COENZYME A SYNTHETASE 2A / BUTYRATE--COA LIGASE 2A


Mass: 63334.562 Da / Num. of mol.: 3 / Fragment: RESIDUES 32-577 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: MITOCHONDRIA / Plasmid: PFB-LIC-BSE / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q08AH3, medium-chain acyl-CoA ligase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 655 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 64 TO PRO ENGINEERED RESIDUE IN CHAIN B, LEU 64 TO PRO ...ENGINEERED RESIDUE IN CHAIN A, LEU 64 TO PRO ENGINEERED RESIDUE IN CHAIN B, LEU 64 TO PRO ENGINEERED RESIDUE IN CHAIN C, LEU 64 TO PRO

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.2 % / Description: NONE
Crystal growDetails: 0.2M AMMONIUM ACETATE, 0.1M TRIS PH 8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418
DetectorType: RIGAKU AREA DETECTOR / Date: Mar 18, 2008 / Details: OSMIC
RadiationMonochromator: NI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→37.99 Å / Num. obs: 73402 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 9.58
Reflection shellResolution: 2.45→2.71 Å / Redundancy: 3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B7W
Resolution: 2.45→39.16 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.901 / SU B: 16.992 / SU ML: 0.202 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.491 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 3454 5 %RANDOM
Rwork0.193 ---
obs0.196 65612 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 1.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.45→39.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12382 0 70 655 13107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02212863
X-RAY DIFFRACTIONr_bond_other_d0.0020.028684
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.9717504
X-RAY DIFFRACTIONr_angle_other_deg0.919321250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82151624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14624.36516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.966152188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.281564
X-RAY DIFFRACTIONr_chiral_restr0.1120.21959
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214202
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022467
X-RAY DIFFRACTIONr_nbd_refined0.210.22610
X-RAY DIFFRACTIONr_nbd_other0.1980.28872
X-RAY DIFFRACTIONr_nbtor_refined0.180.26087
X-RAY DIFFRACTIONr_nbtor_other0.0850.26631
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2594
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1940.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.38138379
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.596512980
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.95185423
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.581104514
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1460tight positional0.040.05
12B1460tight positional0.040.05
13C1460tight positional0.050.05
21A322tight positional0.040.05
22B322tight positional0.040.05
23C322tight positional0.040.05
51A174tight positional0.040.05
52B174tight positional0.040.05
53C174tight positional0.040.05
31A1577medium positional0.170.5
41A283medium positional0.150.5
42B283medium positional0.180.5
43C283medium positional0.180.5
11A1665loose positional0.235
12B1665loose positional0.215
13C1665loose positional0.295
21A369loose positional0.445
22B369loose positional0.325
23C369loose positional0.295
51A217loose positional0.175
52B217loose positional0.155
53C217loose positional0.175
11A1460tight thermal00.5
12B1460tight thermal00.5
13C1460tight thermal00.5
21A322tight thermal00.5
22B322tight thermal00.5
23C322tight thermal00.5
51A174tight thermal00.5
52B174tight thermal00.5
53C174tight thermal00.5
31A1577medium thermal0.152
41A283medium thermal0.082
42B283medium thermal0.042
43C283medium thermal0.042
11A1665loose thermal0.810
12B1665loose thermal0.9810
13C1665loose thermal0.8810
21A369loose thermal1.2510
22B369loose thermal0.8510
23C369loose thermal1.2710
51A217loose thermal0.3710
52B217loose thermal0.310
53C217loose thermal0.4210
LS refinement shellResolution: 2.45→2.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 243 -
Rwork0.289 4620 -
obs--100 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.5525-2.06260.90522.98590.30833.22120.10560.36110.1626-0.396-0.1524-0.0371-0.0961-0.27010.0468-0.0299-0.06150.0396-0.03720.0514-0.0602-39.133821.658-18.9591
21.50960.0996-0.07061.3780.59492.42220.0353-0.0885-0.12630.0325-0.0390.12240.2136-0.24520.0037-0.0668-0.01030.0061-0.05060.0274-0.063-44.274722.5551-0.8886
32.7377-0.1785-1.01731.46640.46982.1756-0.0480.06180.141-0.0235-0.0547-0.3166-0.04060.040.10280.0117-0.017-0.0046-0.1262-0.0042-0.0753-26.851421.7133-12.3272
41.03870.228-0.41273.58410.25241.13020.05420.02-0.0355-0.1338-0.0422-0.23340.00390.0332-0.0119-0.0064-0.0010.0048-0.060.0326-0.0933-21.876938.5204-8.0843
51.72370.04190.55672.8474-0.92825.14690.0827-0.16-0.0716-0.0886-0.1264-0.1690.18310.45190.0437-0.0871-0.00060.0071-0.01580.0399-0.0584-21.173929.67517.7406
60.9882-2.69610.893511.00741.194.45890.0612-0.07170.2559-0.06680.0351-0.3996-0.59310.3051-0.0964-0.0598-0.1113-0.01380.05430.02020.1035-17.544642.821319.8189
72.46371.96480.27724.3271-0.89313.0144-0.05420.20760.1931-0.08630.0533-0.1301-0.54370.12120.00080.00790.0378-0.0317-0.0416-0.0342-0.0393-26.6039-7.35911.1139
82.0173-0.23350.59371.57050.01563.0472-0.0316-0.33140.37840.0748-0.09640.2019-0.3502-0.31950.128-0.00870.025-0.00790.024-0.12640.0105-26.3544-3.100129.2453
91.65070.45120.53122.68781.45621.81030.0392-0.0839-0.02250.0831-0.0575-0.0610.07140.07060.0183-0.09520.0321-0.0167-0.0299-0.0078-0.0944-27.1139-20.165916.9453
102.58770.20890.66211.38980.57321.3715-0.0453-0.0158-0.0653-0.01460.06420.04990.01270.1256-0.0188-0.06740.00750.0164-0.00760-0.1259-10.359-25.229621.2243
113.4762-1.3966-1.72881.23790.51095.7551-0.46550.0804-0.45280.28870.06320.32440.92780.04990.40230.1624-0.00320.09360.083-0.0492-0.007-19.755-26.860246.8771
127.6272-3.8209-0.9611.91710.42431.2393-0.596-0.4163-0.6007-0.1706-0.0882-0.36510.751.30630.68420.42150.23170.0310.3443-0.00990.1274-6.5109-30.671249.0941
135.13512.9265-0.31035.2619-1.29033.67220.0475-0.90830.25780.7259-0.13110.0549-0.0026-0.5890.08350.13980.1092-0.06380.2137-0.06170.01917.754223.170450.7655
142.4934-0.3396-0.10831.8386-0.07082.8695-0.0594-0.06430.31010.04440.0350.1463-0.2433-0.3320.0244-0.0135-0.0016-0.06830.01610.02040.00555.501324.362832.5391
155.0158-0.38111.43133.13270.4961.0196-0.2228-0.24710.39890.3176-0.0177-0.517-0.1008-0.13730.24050.10550.0141-0.144-0.0255-0.04420.093820.955924.782246.3617
163.39380.58781.5593.76130.5642.30090.1094-0.0728-0.0130.445-0.113-0.480.15770.04160.00370.0780.0115-0.1079-0.01790.06110.03227.1148.455641.6135
173.26641.3346-2.80212.5844-1.21012.87770.163-0.1198-0.0690.2347-0.1013-0.15220.02270.2173-0.0618-0.04120.0043-0.06750.0330.05940.029830.776719.663515.7494
1812.53498.28298.47738.420910.022321.0455-0.2202-0.3014-0.88670.74340.39960.58751.10690.8399-0.17940.17210.1423-0.02980.09720.18040.539133.98155.464815.4042
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 84
2X-RAY DIFFRACTION2A85 - 241
3X-RAY DIFFRACTION3A242 - 305
4X-RAY DIFFRACTION4A306 - 461
5X-RAY DIFFRACTION5A462 - 544
6X-RAY DIFFRACTION6A545 - 569
7X-RAY DIFFRACTION7B37 - 87
8X-RAY DIFFRACTION8B88 - 241
9X-RAY DIFFRACTION9B242 - 305
10X-RAY DIFFRACTION10B306 - 461
11X-RAY DIFFRACTION11B462 - 545
12X-RAY DIFFRACTION12B546 - 569
13X-RAY DIFFRACTION13C34 - 84
14X-RAY DIFFRACTION14C85 - 241
15X-RAY DIFFRACTION15C242 - 305
16X-RAY DIFFRACTION16C306 - 462
17X-RAY DIFFRACTION17C463 - 553
18X-RAY DIFFRACTION18C554 - 569

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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

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