[English] 日本語
Yorodumi
- PDB-6p4x: Crystal Structure of the S. cerevisiae glucokinase, Glk1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p4x
TitleCrystal Structure of the S. cerevisiae glucokinase, Glk1
ComponentsGlucokinase-1
KeywordsTRANSFERASE / hexokinase / actin atpase / glycolysis
Function / homology
Function and homology information


Regulation of Glucokinase by Glucokinase Regulatory Protein / Synthesis of GDP-mannose / glucokinase / Glycolysis / fructokinase activity / glucokinase activity / mannose metabolic process / glucose 6-phosphate metabolic process / D-glucose binding / D-glucose import ...Regulation of Glucokinase by Glucokinase Regulatory Protein / Synthesis of GDP-mannose / glucokinase / Glycolysis / fructokinase activity / glucokinase activity / mannose metabolic process / glucose 6-phosphate metabolic process / D-glucose binding / D-glucose import / intracellular glucose homeostasis / Neutrophil degranulation / glycolytic process / glucose metabolic process / mitochondrion / ATP binding / plasma membrane / cytosol
Similarity search - Function
Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. ...Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Glucokinase-1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59 Å
AuthorsStoddard, P.R. / Garner, E.C. / Murray, A.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31GM116441 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2AI117923 United States
CitationJournal: Science / Year: 2020
Title: Polymerization in the actin ATPase clan regulates hexokinase activity in yeast.
Authors: Patrick R Stoddard / Eric M Lynch / Daniel P Farrell / Annie M Dosey / Frank DiMaio / Tom A Williams / Justin M Kollman / Andrew W Murray / Ethan C Garner /
Abstract: The actin fold is found in cytoskeletal polymers, chaperones, and various metabolic enzymes. Many actin-fold proteins, such as the carbohydrate kinases, do not polymerize. We found that Glk1, a ...The actin fold is found in cytoskeletal polymers, chaperones, and various metabolic enzymes. Many actin-fold proteins, such as the carbohydrate kinases, do not polymerize. We found that Glk1, a glucokinase, forms two-stranded filaments with ultrastructure that is distinct from that of cytoskeletal polymers. In cells, Glk1 polymerized upon sugar addition and depolymerized upon sugar withdrawal. Polymerization inhibits enzymatic activity; the Glk1 monomer-polymer equilibrium sets a maximum rate of glucose phosphorylation regardless of Glk1 concentration. A mutation that eliminated Glk1 polymerization alleviated concentration-dependent enzyme inhibition. Yeast containing nonpolymerizing Glk1 were less fit when growing on sugars and more likely to die when refed glucose. Glk1 polymerization arose independently from other actin-related filaments and may allow yeast to rapidly modulate glucokinase activity as nutrient availability changes.
History
DepositionMay 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 22, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.3Oct 11, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucokinase-1
B: Glucokinase-1
C: Glucokinase-1
D: Glucokinase-1
E: Glucokinase-1
F: Glucokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,91219
Polymers332,6786
Non-polymers1,23513
Water00
1
A: Glucokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7314
Polymers55,4461
Non-polymers2853
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6363
Polymers55,4461
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glucokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6363
Polymers55,4461
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glucokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6363
Polymers55,4461
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Glucokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6363
Polymers55,4461
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Glucokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6363
Polymers55,4461
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
A: Glucokinase-1
C: Glucokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3677
Polymers110,8932
Non-polymers4755
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-32 kcal/mol
Surface area43020 Å2
MethodPISA
8
B: Glucokinase-1
E: Glucokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2726
Polymers110,8932
Non-polymers3804
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-29 kcal/mol
Surface area41920 Å2
MethodPISA
9
D: Glucokinase-1
F: Glucokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2726
Polymers110,8932
Non-polymers3804
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-27 kcal/mol
Surface area43400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.750, 177.750, 323.947
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPPROPRO(chain 'A' and (resid 4 through 119 or (resid 120...AA4 - 504 - 50
12LYSLYSVALVAL(chain 'A' and (resid 4 through 119 or (resid 120...AA60 - 49960 - 499
23ASPASPPROPRO(chain 'B' and (resid 4 through 50 or resid 60...BB4 - 504 - 50
24LYSLYSVALVAL(chain 'B' and (resid 4 through 50 or resid 60...BB60 - 49960 - 499
35ASPASPPROPRO(chain 'C' and (resid 4 through 50 or resid 60...CC4 - 504 - 50
36LYSLYSVALVAL(chain 'C' and (resid 4 through 50 or resid 60...CC60 - 49960 - 499
47ASPASPPROPRO(chain 'D' and (resid 4 through 119 or (resid 120...DD4 - 504 - 50
48LYSLYSVALVAL(chain 'D' and (resid 4 through 119 or (resid 120...DD60 - 49960 - 499
59ASPASPPROPRO(chain 'E' and (resid 4 through 119 or (resid 120...EE4 - 504 - 50
510LYSLYSVALVAL(chain 'E' and (resid 4 through 119 or (resid 120...EE60 - 49960 - 499
611ASPASPPROPRO(chain 'F' and (resid 4 through 50 or resid 60...FF4 - 504 - 50
612LYSLYSVALVAL(chain 'F' and (resid 4 through 50 or resid 60...FF60 - 49960 - 499

-
Components

#1: Protein
Glucokinase-1 / Glucose kinase 1 / GLK-1


Mass: 55446.258 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: GLK1, HOR3, YCL040W, YCL312, YCL40W / Production host: Escherichia coli (E. coli) / References: UniProt: P17709, glucokinase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: PO4
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.92 Å3/Da / Density % sol: 68.59 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9.4 / Details: 2.4M Diammonium Phosphate, 0.1M CHES pH 9.4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.59→155.83 Å / Num. obs: 61332 / % possible obs: 99.97 % / Redundancy: 2 % / Biso Wilson estimate: 91.07 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.1003 / Rpim(I) all: 0.1003 / Rrim(I) all: 0.1418 / Net I/σ(I): 8.28
Reflection shellResolution: 3.59→3.718 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4831 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 6026 / CC1/2: 0.638 / Rpim(I) all: 0.4831 / Rrim(I) all: 0.6832 / % possible all: 99.95

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Coot1.14_3260model building
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IG8

1ig8


Resolution: 3.59→155.83 Å / SU ML: 0.5282 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.4634
RfactorNum. reflection% reflection
Rfree0.3002 3105 5.06 %
Rwork0.2668 --
obs0.2685 61322 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 85.05 Å2
Refinement stepCycle: LAST / Resolution: 3.59→155.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22948 0 5 0 22953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004823359
X-RAY DIFFRACTIONf_angle_d1.490331600
X-RAY DIFFRACTIONf_chiral_restr0.07543628
X-RAY DIFFRACTIONf_plane_restr0.00624066
X-RAY DIFFRACTIONf_dihedral_angle_d20.29148733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.59-3.650.34221490.33952609X-RAY DIFFRACTION99.96
3.65-3.710.38431520.33282563X-RAY DIFFRACTION99.93
3.71-3.770.32681450.33022603X-RAY DIFFRACTION99.96
3.77-3.840.38711280.34312591X-RAY DIFFRACTION99.96
3.84-3.910.35931260.32372622X-RAY DIFFRACTION99.93
3.91-3.990.331320.31292625X-RAY DIFFRACTION100
3.99-4.080.35061450.28792592X-RAY DIFFRACTION99.96
4.08-4.170.34171370.28952607X-RAY DIFFRACTION100
4.17-4.280.30971380.28182624X-RAY DIFFRACTION100
4.28-4.390.27271360.2642630X-RAY DIFFRACTION100
4.39-4.520.29941400.25942619X-RAY DIFFRACTION100
4.52-4.670.28661560.24542632X-RAY DIFFRACTION100
4.67-4.840.29721540.252604X-RAY DIFFRACTION99.96
4.84-5.030.26361660.26112616X-RAY DIFFRACTION100
5.03-5.260.31621420.27022633X-RAY DIFFRACTION100
5.26-5.540.32871350.29342648X-RAY DIFFRACTION99.96
5.54-5.880.30191300.29572674X-RAY DIFFRACTION100
5.88-6.340.33711290.29712681X-RAY DIFFRACTION100
6.34-6.970.32951370.26772691X-RAY DIFFRACTION100
6.97-7.980.28131530.23922687X-RAY DIFFRACTION99.96
7.98-10.060.20791280.18822765X-RAY DIFFRACTION100
10.06-155.830.2591470.22352901X-RAY DIFFRACTION99.67
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)
11.41539467756-0.8316608186310.5924547574860.548081245692-0.1882619469981.03304542759-0.0926001556018-0.1416066796650.1253321153740.5395037260350.278279550982-0.5071490312370.01010442804360.3443445861170.1302592125530.5700780160670.00139753022022-0.06301303844180.4123346577510.03345928464620.957352135841-34.702604476754.9198599216-52.8552130225
21.724217833610.76001459642-0.569465977021.470208355430.03555016583242.82370687699-0.3375230773310.839880869050.0406101827137-0.01848846866080.3413291963350.407704931589-0.1703184014330.3280366348750.1450216023340.5577780369110.130502831186-0.01033629719520.3203483648270.06248239841150.797742020819-56.68502994928.9045508078-17.2268153902
30.674872971869-0.273118062104-0.6072185732150.8877555293020.05913283535441.11390785171-0.595905409811-0.784853107614-0.004188365260791.096178251740.03076942064360.7685180482380.243931940863-0.1388732401020.2060585871910.9530753432280.03925121021860.3864750976350.468827679922-0.05382449959231.32732142199-78.45481392578.351321175854.1332214162
41.26224634680.07730942510120.2679855636661.57994095197-0.1164430145361.93390808142-0.304768730447-0.4511937591-0.6097987844320.684395215060.439248667720.5575763301120.4774650970760.3167662063190.2116184773690.9372343381360.09315873718520.2832410900240.5926281626910.103590313941.06599511606-72.9987523350.119832021517-2.23695892851
51.62767351557-0.152555660555-0.1691219956451.03618311122-0.2148464954220.5865760872790.0445949977783-0.0576358815525-0.6347894909540.4219882690730.0487549064353-0.1255185991960.3748725086250.2288598547150.1958078260960.662013194270.0813980904977-0.04621321918720.3247992020380.05363070876890.834290642774-54.855803250822.924427619-9.28585533144
61.163290096430.485211159595-0.7558023378881.045726701140.5135037430081.29588455725-0.110391650425-0.225904367761-0.1480316822560.424647914623-0.1313435357010.333425051705-0.189281405526-0.2758940727940.1609570834030.7944878258380.1377320385170.04334859197930.3658459274920.004115260427980.782417433262-67.993827519329.192511657-9.05338748491
71.11581406912-0.830692932586-0.3023438390452.43161922540.3355949377411.79533034326-0.226188032621-0.1044961981560.441784176490.49282388801-0.08325112893630.775749592705-0.1253963675760.4245535543210.1329631711080.608924743502-0.0675534514601-0.2624193680290.3885094220860.08527427788050.709811803782-34.219727109249.7763000117-23.7547028156
80.860620377153-0.312539100933-0.5175885339110.5396391285890.5749834591340.656150556306-0.0053667509079-0.1012830655270.530463727222-0.02989902876790.222699541544-0.5432219888410.8402261353181.061498600320.1928732818111.26229756918-0.120925643748-0.1807208366081.512049332590.05302636990181.70127587392-0.67641540981759.8266262505-27.0485620678
90.9731260966930.0965130141414-0.2150136099353.26637507061-0.03118005859531.08118251039-0.07969010852320.04975913364080.1688582554230.344344985211-0.0136656542273-0.558707764633-0.2850892289420.3561474194970.1369802136440.538080605243-0.0493415384531-0.2050885448570.4272682904390.04124263012610.893925350318-25.213522148551.3098721785-28.3772496067
101.25057270106-0.204611913607-0.3554262174481.342493942470.6671861648661.46867415617-0.124527204239-0.01378231368390.4988093375520.2902140510130.0202647862190.180524158871-0.311856493672-0.229541060833-0.1190957410820.6637443772890.09785110971150.01635803327120.5939405004760.006615396664550.886257724374-85.0657055023103.663344082-51.5367273835
111.598229751930.0191122376724-0.7472611852511.711723869570.8279405779411.26012731863-0.0186989322820.05284565536820.2279205356490.2046237923430.02264981372090.144970068231-0.0404958963103-0.397979310038-0.04495048802180.5931110059780.148923563489-0.06162155895090.3665665293050.04714665923030.606696170163-79.788046572490.5532602158-52.2646273394
121.31332210916-0.7000727327050.6603635048020.575502790551-0.2021119886312.55815240062-0.27119890358-0.263732261712-0.3156304517870.3320763962960.2415757392020.2763868575310.383778390262-0.1148711518230.05802895532550.8783255280520.1230912207190.1849772549120.4897357137060.06220011450260.927890935017-91.173769582443.668985903414.4208650249
131.42791788614-0.8947974245830.2452841642371.40212292687-0.009733713194211.99606550222-0.16017626862-0.304249388937-0.3787953510830.2594774507050.1785980663410.06452244979770.376675495579-0.2403664563870.03890152903940.7077680896570.007423940575570.1130154281240.400925119912-0.02237985819410.76879389619-90.008028683244.96961243542.0569919266
141.06385188799-0.348074783223-0.6872103652531.6128051397-0.7441232629231.10018387118-0.1797485777490.332967413256-0.284658439967-0.2995246110490.02122122563860.2076928600530.1407634852790.5730965782590.001220412710190.502077471807-0.00210591945603-0.0780190834170.777920777146-0.2009089753050.739961273511-100.23380077458.8689430678-32.6969209971
150.790498132472-0.891007159603-1.307608674220.986376415321.445322156322.084006811260.3542612038170.749491942873-0.0247159500084-0.671355091242-0.2536095162121.455416821380.183558948799-0.974927786304-0.08997573778521.2862681170.0908340168171-0.3488989307481.998194214930.2418248240221.70916431308-125.48063900971.785410042-58.5174319247
160.8159567744940.146930566034-1.051133740950.997974427262-0.3688405317712.321151162360.01316384088190.4102095529720.122429610974-0.3392818294820.1280476571330.300526797773-0.0687097478291-0.602258302641-0.02925018885050.637598357647-0.0238988591529-0.0865108430030.816393953437-0.1221774447780.80480325865-105.62103925267.687895453-40.4649790841
170.889833269903-0.1032014501720.494881823891.861464499960.2035547239091.10081533062-0.185386215329-0.01412098798760.1719478198870.2285028671610.07306121059360.06340879797620.03045158360640.1227009415650.08138035568060.527019957018-0.04589610254170.02371523826270.2703747645310.0003483732972220.775236431751-41.754718149362.7668133052-61.3308382005
181.372306625840.946215350486-0.8125615050322.596469752760.08920582849171.44410558786-0.2967636347080.3709186236520.141412313582-0.318632281210.315210663817-0.395120169193-0.2508746581560.699032820350.1834850978430.545942564008-0.04555676545730.07502589165640.921655056927-0.01306058317541.16415556374-20.620902823153.1872187798-79.2435009912
191.02843614318-1.59396045664-0.06323740752072.807409731130.3804723105661.344006100910.008963824135340.1821233112110.0287150110074-0.2266470903820.031067126467-0.288227322553-0.1861278171820.1753202442930.06611473287620.461645704424-0.119291058509-0.0496412836930.3152979389050.02514505227970.711343345821-41.197976841867.241963017-61.7203421823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 433 through 500 )
2X-RAY DIFFRACTION2chain 'B' and (resid 3 through 75 )
3X-RAY DIFFRACTION3chain 'B' and (resid 76 through 109 )
4X-RAY DIFFRACTION4chain 'B' and (resid 110 through 241 )
5X-RAY DIFFRACTION5chain 'B' and (resid 242 through 400 )
6X-RAY DIFFRACTION6chain 'B' and (resid 401 through 500 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 80 )
8X-RAY DIFFRACTION8chain 'C' and (resid 81 through 193 )
9X-RAY DIFFRACTION9chain 'C' and (resid 194 through 500 )
10X-RAY DIFFRACTION10chain 'D' and (resid 4 through 193 )
11X-RAY DIFFRACTION11chain 'D' and (resid 194 through 500 )
12X-RAY DIFFRACTION12chain 'E' and (resid 3 through 187 )
13X-RAY DIFFRACTION13chain 'E' and (resid 188 through 500 )
14X-RAY DIFFRACTION14chain 'F' and (resid 1 through 73 )
15X-RAY DIFFRACTION15chain 'F' and (resid 74 through 202 )
16X-RAY DIFFRACTION16chain 'F' and (resid 203 through 500 )
17X-RAY DIFFRACTION17chain 'A' and (resid 1 through 98 )
18X-RAY DIFFRACTION18chain 'A' and (resid 99 through 227 )
19X-RAY DIFFRACTION19chain 'A' and (resid 228 through 432 )

+
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