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- PDB-2qc8: Crystal structure of human glutamine synthetase in complex with A... -

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Basic information

Entry
Database: PDB / ID: 2qc8
TitleCrystal structure of human glutamine synthetase in complex with ADP and methionine sulfoximine phosphate
ComponentsGlutamine synthetase
KeywordsLIGASE / Amino-acid biosynthesis / Synthetase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


protein S-acyltransferase / Astrocytic Glutamate-Glutamine Uptake And Metabolism / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / regulation of protein localization to nucleolus / regulation of sprouting angiogenesis / regulation of endothelial cell migration / glutamate catabolic process / glutamine synthetase / glutamine biosynthetic process ...protein S-acyltransferase / Astrocytic Glutamate-Glutamine Uptake And Metabolism / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / regulation of protein localization to nucleolus / regulation of sprouting angiogenesis / regulation of endothelial cell migration / glutamate catabolic process / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / Glutamate and glutamine metabolism / glial cell projection / response to glucose / cellular response to starvation / ribosome biogenesis / cell body / angiogenesis / cell population proliferation / endoplasmic reticulum / mitochondrion / extracellular exosome / ATP binding / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Glutamine synthetase, N-terminal domain / Glutamine synthetase/guanido kinase, catalytic domain / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. ...Glutamine synthetase, N-terminal domain / Glutamine synthetase/guanido kinase, catalytic domain / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase, N-terminal domain / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain / Ubiquitin-like (UB roll) / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / L-METHIONINE-S-SULFOXIMINE PHOSPHATE / Glutamine synthetase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKarlberg, T. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. ...Karlberg, T. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hogbom, M. / Johansson, I. / Kallas, A. / Kotenyova, T. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Sundstrom, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Holmberg-Schiavone, L. / Structural Genomics Consortium (SGC)
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structures of mammalian glutamine synthetases illustrate substrate-induced conformational changes and provide opportunities for drug and herbicide design.
Authors: Krajewski, W.W. / Collins, R. / Holmberg-Schiavone, L. / Jones, T.A. / Karlberg, T. / Mowbray, S.L.
History
DepositionJun 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamine synthetase
B: Glutamine synthetase
C: Glutamine synthetase
D: Glutamine synthetase
E: Glutamine synthetase
F: Glutamine synthetase
G: Glutamine synthetase
H: Glutamine synthetase
I: Glutamine synthetase
J: Glutamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)442,52470
Polymers433,64810
Non-polymers8,87760
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)181.210, 126.080, 188.170
Angle α, β, γ (deg.)90.00, 92.14, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNVALVAL3AA10 - 5429 - 73
21ASNASNVALVAL3BB10 - 5429 - 73
31ASNASNVALVAL3CC10 - 5429 - 73
41ASNASNVALVAL3DD10 - 5429 - 73
51ASNASNVALVAL3EE10 - 5429 - 73
61ASNASNVALVAL3FF10 - 5429 - 73
71ASNASNVALVAL3GG10 - 5429 - 73
81ASNASNVALVAL3HH10 - 5429 - 73
91ASNASNVALVAL3II10 - 5429 - 73
101ASNASNVALVAL3JJ10 - 5429 - 73
12GLUGLUARGARG3AA56 - 10675 - 125
22GLUGLUARGARG3BB56 - 10675 - 125
32GLUGLUARGARG3CC56 - 10675 - 125
42GLUGLUARGARG3DD56 - 10675 - 125
52GLUGLUARGARG3EE56 - 10675 - 125
62GLUGLUARGARG3FF56 - 10675 - 125
72GLUGLUARGARG3GG56 - 10675 - 125
82GLUGLUARGARG3HH56 - 10675 - 125
92GLUGLUARGARG3II56 - 10675 - 125
102GLUGLUARGARG3JJ56 - 10675 - 125
13PROPROASPASP3AA108 - 122127 - 141
23PROPROASPASP3BB108 - 122127 - 141
33PROPROASPASP3CC108 - 122127 - 141
43PROPROASPASP3DD108 - 122127 - 141
53PROPROASPASP3EE108 - 122127 - 141
63PROPROASPASP3FF108 - 122127 - 141
73PROPROASPASP3GG108 - 122127 - 141
83PROPROASPASP3HH108 - 122127 - 141
93PROPROASPASP3II108 - 122127 - 141
103PROPROASPASP3JJ108 - 122127 - 141
14VALVALHISHIS3AA124 - 281143 - 300
24VALVALHISHIS3BB124 - 281143 - 300
34VALVALHISHIS3CC124 - 281143 - 300
44VALVALHISHIS3DD124 - 281143 - 300
54VALVALHISHIS3EE124 - 281143 - 300
64VALVALHISHIS3FF124 - 281143 - 300
74VALVALHISHIS3GG124 - 281143 - 300
84VALVALHISHIS3HH124 - 281143 - 300
94VALVALHISHIS3II124 - 281143 - 300
104VALVALHISHIS3JJ124 - 281143 - 300
15TYRTYRASNASN3AA283 - 310302 - 329
25TYRTYRASNASN3BB283 - 310302 - 329
35TYRTYRASNASN3CC283 - 310302 - 329
45TYRTYRASNASN3DD283 - 310302 - 329
55TYRTYRASNASN3EE283 - 310302 - 329
65TYRTYRASNASN3FF283 - 310302 - 329
75TYRTYRASNASN3GG283 - 310302 - 329
85TYRTYRASNASN3HH283 - 310302 - 329
95TYRTYRASNASN3II283 - 310302 - 329
105TYRTYRASNASN3JJ283 - 310302 - 329
16PHEPHEGLYGLY4AA312 - 365331 - 384
26PHEPHEGLYGLY4BB312 - 365331 - 384
36PHEPHEGLYGLY4CC312 - 365331 - 384
46PHEPHEGLYGLY4DD312 - 365331 - 384
56PHEPHETHRTHR4EE312 - 364331 - 383
66PHEPHEGLYGLY4FF312 - 365331 - 384
76PHEPHEGLYGLY4GG312 - 365331 - 384
86PHEPHEGLYGLY4HH312 - 365331 - 384
96PHEPHEGLYGLY4II312 - 365331 - 384
106PHEPHEGLYGLY4JJ312 - 365331 - 384

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Components

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
Glutamine synthetase / / Glutamate-ammonia ligase / GS


Mass: 43364.773 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLUL, GLNS / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)gold pRARE2 / References: UniProt: P15104, glutamine synthetase

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Non-polymers , 5 types, 291 molecules

#2: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-P3S / L-METHIONINE-S-SULFOXIMINE PHOSPHATE


Mass: 260.205 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C5H13N2O6PS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 298 K / pH: 7
Details: 1.1M Sodium malonate, 0.5% Jeffamine ED-2001, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.00595
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00595 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 129787 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.12 / Rsym value: 0.092 / Net I/σ(I): 15.6
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.324 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0032refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OJW
Resolution: 2.6→39.94 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 17.298 / SU ML: 0.187 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.827 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 6497 5 %RANDOM
Rwork0.166 ---
obs0.168 123433 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.49 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28146 0 460 231 28837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02229330
X-RAY DIFFRACTIONr_bond_other_d0.0020.0220417
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.95939745
X-RAY DIFFRACTIONr_angle_other_deg0.943349193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.08953549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61623.4031440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.998154740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.46715240
X-RAY DIFFRACTIONr_chiral_restr0.10.24020
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0232893
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026259
X-RAY DIFFRACTIONr_nbd_refined0.2130.26220
X-RAY DIFFRACTIONr_nbd_other0.2020.221699
X-RAY DIFFRACTIONr_nbtor_refined0.1860.214173
X-RAY DIFFRACTIONr_nbtor_other0.0860.215102
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2874
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4380.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2930.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.721.522600
X-RAY DIFFRACTIONr_mcbond_other0.1331.57237
X-RAY DIFFRACTIONr_mcangle_it0.893228445
X-RAY DIFFRACTIONr_scbond_it1.491313824
X-RAY DIFFRACTIONr_scangle_it2.1784.511300
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1732tight positional0.130.05
2B1732tight positional0.130
3C1732tight positional0.110
4D1732tight positional0.120
5E1732tight positional0.120
6F1732tight positional0.120
7G1732tight positional0.120
8H1732tight positional0.120
9I1732tight positional0.120
10J1732tight positional0.120
1A713medium positional0.160.5
2B713medium positional0.180
3C713medium positional0.150
4D713medium positional0.140
5E713medium positional0.140
6F713medium positional0.150
7G713medium positional0.170
8H713medium positional0.170
9I713medium positional0.140
10J713medium positional0.150
1A2309loose positional0.195
2B2309loose positional0.240
3C2309loose positional0.180
4D2309loose positional0.180
5E2309loose positional0.190
6F2309loose positional0.20
7G2309loose positional0.190
8H2309loose positional0.180
9I2309loose positional0.240
10J2309loose positional0.210
1A1732tight thermal0.420.5
2B1732tight thermal0.470
3C1732tight thermal0.480
4D1732tight thermal0.420
5E1732tight thermal0.420
6F1732tight thermal0.330
7G1732tight thermal0.310
8H1732tight thermal0.350
9I1732tight thermal0.350
10J1732tight thermal0.30
1A713medium thermal0.462
2B713medium thermal0.530
3C713medium thermal0.550
4D713medium thermal0.480
5E713medium thermal0.480
6F713medium thermal0.310
7G713medium thermal0.340
8H713medium thermal0.350
9I713medium thermal0.350
10J713medium thermal0.40
1A2309loose thermal0.5910
2B2309loose thermal0.650
3C2309loose thermal0.680
4D2309loose thermal0.610
5E2309loose thermal0.620
6F2309loose thermal0.470
7G2309loose thermal0.460
8H2309loose thermal0.480
9I2309loose thermal0.480
10J2309loose thermal0.470
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 479 -
Rwork0.239 9094 -
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)
10.9585-0.04310.27330.3036-0.09740.2482-0.02570.06440.2027-0.0290.01950.0432-0.0410.0020.0061-0.1653-0.01680.0164-0.07390.00970.0341-48.75533.908-23.587
20.50040.12970.12940.7758-0.01670.03690.0170.0457-0.002-0.0239-0.0260.03940.0199-0.02870.009-0.244-0.0180.0048-0.03310.0026-0.0815-18.3799.749-15.807
30.89240.10450.09740.3287-0.02280.1064-0.01730.0641-0.0864-0.02440.0305-0.0077-0.0351-0.0084-0.0132-0.23130.00650.0175-0.08440.0109-0.0434-31.066-27.392-19.116
40.6912-0.2140.07760.7057-0.11920.03760.00750.0872-0.0726-0.07760.02030.0347-0.02650.0052-0.0278-0.2306-0.02150.0105-0.0413-0.0041-0.0338-69.144-26.438-29.135
50.8690.28160.08470.79160.12960.0479-0.0180.04470.0973-0.08930.01270.0827-0.01560.04660.0053-0.21450.0291-0.0063-0.03130.0307-0.0161-80.17411.226-31.725
61.11110.00730.27310.5265-0.22230.606-0.06750.25350.294-0.0712-0.0002-0.1398-0.27070.04460.06760.101-0.06530.00420.19930.17280.0965-34.08733.892-69.309
70.49740.0339-0.07621.0235-0.10360.36430.01430.2870.1104-0.16040.01630.179-0.0106-0.2341-0.0306-0.0136-0.0172-0.05660.43160.10590.0212-67.12614.135-78.01
80.986-0.22430.02190.7083-0.16790.4044-0.09710.3292-0.1996-0.18890.08110.15040.1821-0.11580.0160.098-0.12320.03280.3118-0.1230.0359-59.075-24.56-76.132
90.89910.4373-0.04390.88230.03470.4542-0.08670.1315-0.2759-0.2134-0.02-0.26120.16890.18020.10680.02320.07170.16540.2653-0.04150.1457-21.19-28.667-66.077
100.6677-0.14740.03361.2717-0.28460.4455-0.00580.19690.0752-0.0911-0.1245-0.3904-0.07390.27080.1304-0.0989-0.08350.07910.37410.12560.1743-5.5727.412-62.003
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 36529 - 384
2X-RAY DIFFRACTION2BB10 - 36529 - 384
3X-RAY DIFFRACTION3CC10 - 36529 - 384
4X-RAY DIFFRACTION4DD10 - 36529 - 384
5X-RAY DIFFRACTION5EE10 - 36429 - 383
6X-RAY DIFFRACTION6FF10 - 36529 - 384
7X-RAY DIFFRACTION7GG10 - 36529 - 384
8X-RAY DIFFRACTION8HH10 - 36529 - 384
9X-RAY DIFFRACTION9II10 - 36529 - 384
10X-RAY DIFFRACTION10JJ10 - 36529 - 384

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  • 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

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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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