[English] 日本語
Yorodumi
- PDB-2vgb: HUMAN ERYTHROCYTE PYRUVATE KINASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vgb
TitleHUMAN ERYTHROCYTE PYRUVATE KINASE
ComponentsPYRUVATE KINASE ISOZYMES R/L
KeywordsTRANSFERASE / METAL-BINDING / PHOSPHORYLATION / PYRUVATE KINASE IN THE ACTIVE R-STATE / KINASE / PYRUVATE / MAGNESIUM / GLYCOLYSIS / DISEASE MUTATION
Function / homology
Function and homology information


pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / Pyruvate metabolism / monosaccharide binding / response to metal ion / Glycolysis ...pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / Pyruvate metabolism / monosaccharide binding / response to metal ion / Glycolysis / response to ATP / Regulation of gene expression in beta cells / potassium ion binding / response to glucose / response to cAMP / cellular response to epinephrine stimulus / response to nutrient / glycolytic process / cellular response to insulin stimulus / kinase activity / response to hypoxia / magnesium ion binding / extracellular exosome / ATP binding / cytosol / cytoplasm
Similarity search - Function
PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain ...PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
1,6-di-O-phosphono-beta-D-fructofuranose / : / : / 2-PHOSPHOGLYCOLIC ACID / Pyruvate kinase PKLR
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsValentini, G. / Chiarelli, L. / Fortin, R. / Dolzan, M. / Galizzi, A. / Abraham, D.J. / Wang, C. / Bianchi, P. / Zanella, A. / Mattevi, A.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structure and Function of Human Erythrocyte Pyruvate Kinase. Molecular Basis of Nonspherocytic Hemolytic Anemia.
Authors: Valentini, G. / Chiarelli, L.R. / Fortin, R. / Dolzan, M. / Galizzi, A. / Abraham, D.J. / Wang, C. / Bianchi, P. / Zanella, A. / Mattevi, A.
History
DepositionNov 12, 2007Deposition site: PDBE / Processing site: PDBE
SupersessionNov 20, 2007ID: 1LIU
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 16, 2018Group: Data collection / Category: diffrn_detector / diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 2.0May 1, 2024Group: Atomic model / Derived calculations / Category: atom_site / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr1_label_atom_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PYRUVATE KINASE ISOZYMES R/L
B: PYRUVATE KINASE ISOZYMES R/L
C: PYRUVATE KINASE ISOZYMES R/L
D: PYRUVATE KINASE ISOZYMES R/L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,25820
Polymers227,8974
Non-polymers2,36116
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21560 Å2
ΔGint-47.1 kcal/mol
Surface area89210 Å2
MethodPQS
Unit cell
Length a, b, c (Å)74.413, 172.058, 85.512
Angle α, β, γ (deg.)90.00, 92.46, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33C
43D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNGLUGLU1AA57 - 16111 - 115
211GLNGLNGLUGLU1BB57 - 16111 - 115
311GLNGLNGLUGLU1CC57 - 16111 - 115
411GLNGLNGLUGLU1DD57 - 16111 - 115
121LEULEUALAALA1AA261 - 430215 - 384
221LEULEUALAALA1BB261 - 430215 - 384
321LEULEUALAALA1CC261 - 430215 - 384
421LEULEUALAALA1DD261 - 430215 - 384
131FBPFBPFBPFBP4AE580
231FBPFBPFBPFBP4BI580
331FBPFBPFBPFBP4CM580
431FBPFBPFBPFBP4DQ580
112ILEILEASPASP4AA162 - 260116 - 214
212ILEILEASPASP4BB162 - 260116 - 214
312ILEILEASPASP4CC162 - 260116 - 214
412ILEILEASPASP4DD162 - 260116 - 214
113ALAALAILEILE1AA431 - 573385 - 527
213ALAALAILEILE1BB431 - 573385 - 527
313ALAALAILEILE1CC431 - 573385 - 527
413ALAALAILEILE1DD431 - 573385 - 527
123PGAPGAPGAPGA4AF581
223PGAPGAPGAPGA4BJ581
323PGAPGAPGAPGA4CN581
423PGAPGAPGAPGA4DR581

NCS ensembles :
ID
1
2
3

-
Components

-
Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
PYRUVATE KINASE ISOZYMES R/L / R-TYPE/L-TYPE PYRUVATE KINASE / RED CELL/LIVER PYRUVATE KINASE / PYRUVATE KINASE 1 / PYRUVATE KINASE


Mass: 56974.324 Da / Num. of mol.: 4 / Fragment: RESIDUES 47-574
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P30613, pyruvate kinase
#2: Sugar
ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 4 types, 77 molecules

#3: Chemical
ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.5 Å3/Da / Density % sol: 50.46 % / Description: NONE
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: RECOMBINANT WILD-TYPE RPK WAS CRYSTALLIZED USING THE VAPOR DIFFUSION METHOD AT 22 C. WELL SOLUTIONS CONSISTED OF 50 MM MES/KOH, PH 6.4, 10 MM MNSO4, AND 10-14% W/V PEG8000. HANGING DROPS ...Details: RECOMBINANT WILD-TYPE RPK WAS CRYSTALLIZED USING THE VAPOR DIFFUSION METHOD AT 22 C. WELL SOLUTIONS CONSISTED OF 50 MM MES/KOH, PH 6.4, 10 MM MNSO4, AND 10-14% W/V PEG8000. HANGING DROPS WERE FORMED BY MIXING EQUAL VOLUMES OF 12 MG/ML PROTEIN IN 50 MM KCL, 5 MM FBP, 5 MM PHOSPHOGLYCOLATE, 20 MM POTASSIUM PHOSPHATE, PH 7.0, AND WELL SOLUTIONS.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Type: ESRF / Wavelength: 1
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 55091 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.4
Reflection shellResolution: 2.7→2.7 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.4 / % possible all: 86.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PKN

1pkn


Resolution: 2.73→20 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.881 / SU B: 35.492 / SU ML: 0.332 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2780 5.1 %RANDOM
Rwork0.227 ---
obs0.229 52174 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20.12 Å2
2--0.2 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.73→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15423 0 124 65 15612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02215782
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.97721409
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.42352029
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01123.014657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.809152668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.11615158
X-RAY DIFFRACTIONr_chiral_restr0.0950.22490
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211775
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2570.27652
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.210829
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2658
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.540.2116
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3150.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3991.510104
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.785216275
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.54635710
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5644.55134
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
11A2066tight positional0.070.05
12B2066tight positional0.060.05
13C2066tight positional0.060.05
14D2066tight positional0.050.05
31A1112tight positional0.040.05
32B1112tight positional0.040.05
33C1112tight positional0.050.05
34D1112tight positional0.050.05
11A20medium positional0.280.5
12B20medium positional0.620.5
13C20medium positional0.430.5
14D20medium positional0.350.5
21A541medium positional0.40.5
22B541medium positional0.30.5
23C541medium positional0.230.5
24D541medium positional0.250.5
31A9medium positional0.260.5
32B9medium positional0.240.5
33C9medium positional0.190.5
34D9medium positional0.350.5
11A2066tight thermal0.090.5
12B2066tight thermal0.090.5
13C2066tight thermal0.10.5
14D2066tight thermal0.10.5
31A1112tight thermal0.080.5
32B1112tight thermal0.070.5
33C1112tight thermal0.090.5
34D1112tight thermal0.080.5
11A20medium thermal0.832
12B20medium thermal1.252
13C20medium thermal1.172
14D20medium thermal0.812
21A541medium thermal0.412
22B541medium thermal0.362
23C541medium thermal0.442
24D541medium thermal0.462
31A9medium thermal0.282
32B9medium thermal0.462
33C9medium thermal0.312
34D9medium thermal0.382
LS refinement shellResolution: 2.73→2.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.384 151
Rwork0.334 3194
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)
11.8780.14281.07191.86840.44681.57890.22090.155-0.3718-0.0067-0.0333-0.03360.38190.1085-0.1876-0.16390.07350.02770.003-0.0118-0.104427.9022-6.568637.336
210.1872-0.0612-0.344311.67321.738110.77030.23670.76911.2113-0.05180.1215-1.7249-0.14130.2198-0.3582-0.0942-0.03020.08050.26780.14690.520249.927324.154433.9283
32.21210.36381.14391.8136-0.33822.19070.1057-0.3222-0.37990.40010.0935-0.17030.1305-0.0997-0.1991-0.021-0.0130.06-0.10040.0735-0.0433-6.8293-27.927912.4788
413.7967-0.4967-0.48989.8383-1.948417.6017-1.0607-0.00250.3386-0.08121.29461.9249-0.3117-2.5602-0.23390.0613-0.09420.17660.74330.31640.6573-40.3889-19.53932.0063
51.1948-0.24060.63421.37-0.292.1764-0.03750.02080.1438-0.0874-0.02530.0986-0.1245-0.0410.0628-0.18850.00130.0353-0.1358-0.0331-0.12589.017827.288230.8966
67.37040.0833-0.05826.44120.75595.92730.0701-0.4608-0.4480.68010.1267-0.06650.3466-0.056-0.19680.1113-0.03930.03360.014-0.0012-0.117515.561521.180367.4129
71.13830.32730.28162.75470.53320.8158-0.0934-0.04380.22940.168-0.00840.1378-0.1126-0.03770.1018-0.1963-0.00210.0132-0.10630.0236-0.1328-11.00036.2724-6.7195
85.65131.9334-0.64958.069-1.33366.46760.02440.3304-0.2735-1.10820.0727-0.28860.55380.2116-0.09710.1643-0.04160.0659-0.011-0.0207-0.048-4.3537-22.6928-29.6628
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A57 - 160
2X-RAY DIFFRACTION1A261 - 573
3X-RAY DIFFRACTION2A161 - 260
4X-RAY DIFFRACTION3B57 - 160
5X-RAY DIFFRACTION3B261 - 573
6X-RAY DIFFRACTION4B161 - 260
7X-RAY DIFFRACTION5C57 - 160
8X-RAY DIFFRACTION5C261 - 573
9X-RAY DIFFRACTION6C161 - 260
10X-RAY DIFFRACTION7D57 - 160
11X-RAY DIFFRACTION7D261 - 573
12X-RAY DIFFRACTION8D161 - 260

+
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://pdbjlc1.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