[English] 日本語
Yorodumi
- PDB-8gk6: Crystal structure of extracellular domain of CNNM4 from Echinococ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gk6
TitleCrystal structure of extracellular domain of CNNM4 from Echinococcus granulosus
ComponentsMetal transporter CNNM4
KeywordsMETAL TRANSPORT / Immunoglobulin-like fold / beta-sandwich / Magnesium transporter
Function / homology
Function and homology information


magnesium ion homeostasis / membrane
Similarity search - Function
Ancient conserved domain protein family / Ion transporter-like, CBS domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / CBS domain superfamily / CBS domain / CBS domain profile.
Similarity search - Domain/homology
Metal transporter CNNM4
Similarity search - Component
Biological speciesEchinococcus granulosus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsShahsavan, A. / Gehring, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Protein Sci. / Year: 2024
Title: Dimerization of the CNNM extracellular domain.
Authors: Shahsavan, A. / Lee, E.L. / Illes, K. / Kozlov, G. / Gehring, K.
History
DepositionMar 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metal transporter CNNM4
B: Metal transporter CNNM4
C: Metal transporter CNNM4
D: Metal transporter CNNM4
E: Metal transporter CNNM4
F: Metal transporter CNNM4
H: Metal transporter CNNM4
G: Metal transporter CNNM4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,73519
Polymers124,5078
Non-polymers4,22811
Water73941
1
A: Metal transporter CNNM4
E: Metal transporter CNNM4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3616
Polymers31,1272
Non-polymers1,2344
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metal transporter CNNM4
G: Metal transporter CNNM4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0223
Polymers31,1272
Non-polymers8951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Metal transporter CNNM4
H: Metal transporter CNNM4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3595
Polymers31,1272
Non-polymers1,2323
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Metal transporter CNNM4
F: Metal transporter CNNM4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9945
Polymers31,1272
Non-polymers8673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.338, 120.764, 95.254
Angle α, β, γ (deg.)90.000, 98.090, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 25 through 152)
d_2ens_1(chain "B" and resid 25 through 152)
d_3ens_1(chain "C" and resid 25 through 152)
d_4ens_1(chain "D" and resid 25 through 152)
d_5ens_1(chain "E" and resid 25 through 152)
d_6ens_1(chain "F" and resid 25 through 152)
d_7ens_1(chain "G" and resid 25 through 152)
d_8ens_1(chain "H" and resid 25 through 152)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNSERA2 - 129
d_21ens_1ASNSERF2 - 129
d_31ens_1ASNSERG1 - 128
d_41ens_1ASNSERK1 - 128
d_51ens_1ASNSERO1 - 128
d_61ens_1ASNSERR1 - 128
d_71ens_1ASNSERX1 - 128
d_81ens_1ASNSERT1 - 128

NCS oper:
IDCodeMatrixVector
1given(0.532416466111, 0.181972157564, 0.826691502609), (-0.197971718829, 0.976303051974, -0.0874045150423), (-0.823006625221, -0.117125934692, 0.555825161597)-27.3483186775, 33.7263670402, 7.09985852171
2given(0.328752054591, 0.223354205218, 0.917624643094), (0.224423035595, -0.962275331807, 0.153819657034), (0.917363825152, 0.155367579654, -0.366475821161)-26.93614748, -12.9352143963, 42.1984640712
3given(0.968944076795, 0.0573532188047, 0.240536866896), (0.0544868053816, -0.998342052371, 0.018556252483), (0.241202330177, -0.00487388547726, -0.970462611932)-9.82943996633, 22.1336677986, 54.1239612595
4given(0.77389140623, 0.107190153147, 0.6241813538), (0.0210715205038, -0.989385202015, 0.14378078125), (0.632967678785, -0.0981182607957, -0.767935364801)1.53466660851, 2.04205593595, 4.07182650829
5given(0.862614796118, 0.157162520174, 0.480828093783), (-0.0756238346684, 0.97989681712, -0.184616530758), (-0.500176717919, 0.122890886771, 0.857158725558)-7.10639091505, 20.318884259, 50.3540662678
6given(0.94887833351, -0.111873980301, -0.295151013428), (-0.100508350588, -0.993499327201, 0.0534523929518), (-0.299212265219, -0.0210546760121, -0.953954255172)-22.9887242087, 34.9176880923, 8.10356504631
7given(0.871650167279, -0.0702354149916, -0.48507006954), (0.0968091965948, 0.994853357342, 0.0299128206592), (0.480472647855, -0.0730327588557, 0.873963529443)-25.1681641536, -15.2898103022, 38.7670863197

-
Components

-
Protein / Non-polymers , 2 types, 49 molecules ABCDEFHG

#1: Protein
Metal transporter CNNM4


Mass: 15563.418 Da / Num. of mol.: 8 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echinococcus granulosus (invertebrata) / Gene: EGR_01344 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: W6USS8
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

-
Sugars , 5 types, 11 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl pH 8.5, 25% (w/v) PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95371 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95371 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 45839 / % possible obs: 97.4 % / Redundancy: 4.7 % / Biso Wilson estimate: 39.41 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.096 / Net I/σ(I): 14
Reflection shellResolution: 2.7→2.72 Å / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1246 / CC1/2: 0.622

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→46.64 Å / SU ML: 0.325 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.1186
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2533 3114 6.79 %
Rwork0.1974 42723 -
obs0.2011 45837 68.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.27 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8067 0 277 41 8385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00478576
X-RAY DIFFRACTIONf_angle_d0.767511759
X-RAY DIFFRACTIONf_chiral_restr0.0541452
X-RAY DIFFRACTIONf_plane_restr0.00461453
X-RAY DIFFRACTIONf_dihedral_angle_d11.9633025
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.655685866191
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.945101274339
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.613856238836
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.915767015908
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.880948365046
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS1.06676162039
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS1.05282360295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.740.3318370.3172502X-RAY DIFFRACTION17.33
2.74-2.790.3052480.3015661X-RAY DIFFRACTION23.32
2.79-2.830.3483450.2992750X-RAY DIFFRACTION26.53
2.83-2.880.3077770.2726949X-RAY DIFFRACTION32.75
2.88-2.940.3261720.27381137X-RAY DIFFRACTION40.03
2.94-30.3245980.27531276X-RAY DIFFRACTION45.72
3-3.070.30891110.27451537X-RAY DIFFRACTION53.3
3.07-3.140.29091250.25221672X-RAY DIFFRACTION59.15
3.14-3.210.30871350.24481730X-RAY DIFFRACTION61.23
3.22-3.30.2961350.24321841X-RAY DIFFRACTION64.64
3.3-3.40.30571360.22561992X-RAY DIFFRACTION69.66
3.4-3.510.28691590.2392145X-RAY DIFFRACTION75.15
3.51-3.630.2831590.21882221X-RAY DIFFRACTION77.8
3.63-3.780.26861880.2072487X-RAY DIFFRACTION87.85
3.78-3.950.26261880.19332629X-RAY DIFFRACTION91.58
3.95-4.160.21192040.16872693X-RAY DIFFRACTION95.01
4.16-4.420.22091980.15262743X-RAY DIFFRACTION96.14
4.42-4.760.20191990.14452676X-RAY DIFFRACTION95.2
4.76-5.240.20132040.14942765X-RAY DIFFRACTION96.96
5.24-60.26122040.17932786X-RAY DIFFRACTION97.3
6-7.550.26221900.20492730X-RAY DIFFRACTION96.02
7.55-46.640.23612020.20532801X-RAY DIFFRACTION98.11
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)
12.292605474860.176646740673-0.8485261609122.95964578933-0.7775355313270.8875997256790.02283562421870.5291837919640.0645844410452-0.278868030930.02349107803730.02059731260050.0693186321955-0.4881669085-0.01283296059850.1958113094940.01804320339520.0227527360410.3864542827420.02850808341430.132731114879-5.29404644423-0.2596315301967.05065043868
20.986113671202-0.0832791418094-0.7084332571831.2291891802-0.2091073012131.859191147040.08658905515340.2722046904880.164860782436-0.307576887163-0.077846742691-0.2156837930370.06611676314740.0460623177284-0.05713677640990.1639384857990.01307679717380.02420528769040.2687672347620.1477126824820.2422416547923.47649140143-3.3801969922513.6674164426
31.29460049092-0.8941197246871.208701663970.622980344434-0.8416160171261.13550027833-0.377468169767-0.7327420327580.9772435013080.119814224434-0.477331909754-0.69151505718-1.017789916030.5073850323150.3071136258960.496684235-0.0705533889114-0.110648240590.6811030052530.07743843616720.656381355227-5.331696225188.2396134699622.4655873242
40.0386129400260.1309680589420.02592463552230.4477880375010.08536846808090.257052049570.00127402697599-0.0286974430846-0.03998611854420.125303753229-0.169079156943-0.1681895185670.1419491963980.195135109782-4.306749355340.148357015260.01061968243950.05621919404030.1698848105780.1934394122070.2718322092591.42531447789-5.7424730880616.0260505269
50.7705063217390.2949898584850.5299150933871.25163589991-0.4977563656420.793530608142-0.113129462615-0.06007707105140.1341182796660.04499738734550.01119264055850.351069051024-0.0393671542051-0.3086104680220.03922023952530.112992847504-0.04193366671920.05551678962310.4045938827950.01193050835470.349588501569-10.0973214189-0.83169259470217.5049150314
64.09807153144-0.887802756601-1.783470318974.00537534564-1.610082840432.72332991553-0.484464322371-0.4089707839150.711880333680.7386712474190.644641725067-0.0480865126992-0.2070612610530.0460152234349-0.04982564925860.3585651093850.280236095913-0.1070900672050.78169275727-0.003171855142820.6807102777174.544263611643.0118421933132.5120805476
71.87264560852-0.185939345405-1.104261732810.172865546602-0.1689335529581.348317171750.2023296937740.2826368856350.517593459601-0.0384019495321-3.57754960734E-50.237130083399-0.2006912801930.02022414182650.1856738617190.143780750647-0.00878144178281-0.07639650340130.183880031840.04023886094240.229818449895-3.767582211314.8643481916513.0142573774
83.177713355351.546622303690.3890049110071.74309269974-0.6333016430361.591398009950.0133615780666-0.4072190480740.355150125558-0.495525449744-0.1593366555180.12194870353-0.0327847249896-0.06969047434710.08913660614250.2880105891180.155742319371-0.0006784327147020.2752953478310.06279308727240.295337622032-22.192021243434.735047409112.4521215438
91.315597767120.0270778930034-1.271429648550.0382071959457-0.2898519860073.088994881610.200581037985-0.100965213834-0.2656625165150.0508932713228-0.05551443528590.224792596977-0.473213010084-0.36569389075-0.03485604206490.3257401790240.0115222931276-0.1704335854390.3135511464590.1031705796820.265455812901-28.032030375531.064742372120.4686180858
102.59697020534-0.7564997576510.9612522806510.4102203315920.3995502512952.791791438540.4037928369790.381642383523-0.085610655219-0.417876833203-0.116743263332-0.1462144024550.215633781275-0.07877377249130.127062168550.333946079210.190522774555-0.02403809485620.3008560845720.01161041087630.224099611736-19.794237662229.78043893629.22956258171
111.601527157020.7489458598830.4353910135420.912884872988-0.5721947626851.190910074340.08471195593260.535621191406-0.0788460860284-0.455759533095-0.289076351034-0.3975788061480.3374451669060.386719632309-0.006893826761950.3756428532590.1997063656890.1008238842570.3165346410020.1139957248220.230004982856-9.9476870854428.403481543413.9026578624
121.81068332219-1.23115265479-0.6928757885650.8391636174710.4691265374390.2669477507970.3403366055190.3064982045891.06686560843-0.271204034850.0563035097252-0.63416201561-0.822496263873-0.15217719051-0.03098230455130.7413246122280.03462099589590.2114157977350.6937704503420.01379396644350.483070519831-9.7034328418641.018267813622.7757070072
131.94569713419-0.3522001903361.040776457382.93071287545-0.2878729303775.7981496106-0.1164257666570.2258098336520.05722370224640.0259905795357-0.00745854785639-0.218200482829-0.0538652791931.049226720830.1208678820010.2921290526830.0332519268957-0.07581565951820.313559768220.05336351171670.116593299648-11.700631053128.228694505624.334571459
140.469348236723-0.0967099087423-0.8510740973320.0203224221040.2089051523452.556729458-0.06716169743130.569706077821-0.055360374551-0.467594706658-0.292121967848-0.2801770415850.6327779841330.09859876976990.008136447990650.3003929647350.1911488593320.07052467340080.485201018393-0.01225708145120.200383788083-15.766118830325.24698389077.64566963424
151.661307517490.5945100362580.09872108229460.594444818460.5990566433752.01190258609-0.178875317452-0.1893131926250.3096241999360.00115369093146-0.02927722233020.131257291173-0.0538578889906-0.1909891478310.259073784540.2783137846840.1330389534240.01101486398580.1935640603330.040316925230.153860147797-18.574567457632.910000621825.1302517492
161.40023287302-0.823966496321-0.7058033859482.14079222865-1.117828319581.77562678687-0.077487961206-0.3636312682831.045181541550.2966656983010.383416161892-1.1696789093-0.1753566580310.67577233374-0.1319014118850.3066018460250.1315594383030.04560861877920.8905006447-0.2342313003710.9537651806442.0306707091832.869727967421.2600952772
170.91228116286-0.5388685628240.5503643244551.8087480405-0.8722223341112.382540284980.1257707193190.5378302209110.3858519814480.293276780798-0.04827530593850.136382897052-0.9247081919850.340594667565-0.1239745859290.5327272979230.08633082472310.06664043916880.3115073735590.09694083497850.55689275048-11.455312930137.807086469214.6695562066
181.15756789329-0.794127065779-0.4564281996341.76986525171.096374096571.669312622180.228631533703-0.02351489076890.144981217837-0.419369503494-0.156702030157-0.257683603644-0.33859370979-0.271231693257-0.04818073931310.2928067020550.2073669841750.07140408386440.4280440625220.1004903797780.508367037961-23.895224431537.97072380120.1357097776
190.906913241980.400173182426-0.7670257965531.05580410952-0.04603657213840.8494833724240.00954350808455-0.0141713099179-0.05752071658790.358086890474-0.2985409136310.06277729185020.0508174504512-0.1995520656170.02494117686580.389846396447-0.1389686706330.1120405869670.162740214896-0.04077354252290.336671508685-18.7876246587-9.9708822537536.7911321651
200.173775321361-0.246700482567-0.1120184244280.3525970552140.1589944116550.07162810093850.703598878906-0.310256128284-1.498511203670.7292377745110.4993950553660.4241695878171.8898191355-0.118220384153-0.1878020927510.927102417943-0.0707173496116-0.2045216435920.3770088798650.02405581038110.58541836267-5.88091010066-18.516849956130.5296619321
211.69826750066-0.112466983026-1.22259332580.3856989724720.2542680338482.03468125836-0.0580529528409-0.153305419998-0.06512539145840.0528667762971-0.101666950826-0.08824387785650.2059161472530.440848722967-0.7390043862870.09786774147960.06499438798510.09802206215360.2159428443340.1198706048960.167375082771-8.4073961327-6.1605614886428.6690383559
221.62795682559-0.337432687094-0.3187266548011.22116934583-0.593404424191.743234252620.04254361024950.01019247796750.2831069324630.32175749261-0.1888594755910.11803397614-0.138273671452-0.04132410948940.1526963147720.213446637149-0.09596358591660.005537175488540.2373890335020.002273976889310.16460151426-15.314774807-8.1951329964233.3999232958
234.47571874813-1.47962371985-1.558204561713.39981227799-2.521886522253.71206148842-0.10728515238-0.5694378748540.02808202782740.221738747089-0.562355247064-0.9168022797730.5663113147181.289840509380.2827112300080.4038648721050.0319548149837-0.05856302354850.5202735647570.005971676467580.5839461812444.70890398281-9.8763338779735.131407408
240.746028106608-0.26097531502-0.4030087375490.99636029207-0.06454918341050.5180010157820.1840582586280.000721404902073-0.421199396190.4249325444140.08808588483770.2738900964550.469478417392-0.3829878847020.08165157527440.31940433556-0.116092368111-0.007342060627580.1930037953590.03285628271680.379147653134-15.4627806521-16.257176068633.7350929008
253.88432220822-0.364693119316-1.296775772212.135411475150.6884985024522.9432325095-0.02131520479110.410833822743-0.2984380253910.125651901376-0.3664547748990.2914209198230.27413023343-1.232091701620.08773591466220.311855404146-0.00797499649716-0.01891746823640.436236177145-0.06018059364090.109917867228-10.86237408921.151942349147.2980854463
261.40321665532-1.304983176420.7642411368233.33403146232-1.217707188530.806183116202-0.122043978413-0.38926185127-0.2130336164210.2009700958460.352922052170.502545436139-0.0286062884998-0.18879223378-0.09254040876550.1977005521370.181037016797-0.01850575369170.4727994714720.01389212130770.203821889289-18.984651038525.95918811944.7611988069
270.996069183190.303791425685-0.8091351983161.75195865578-0.3614308410951.13400664153-0.118618754363-0.2087520737950.05413434756390.4694439232020.00336858062246-0.130107812715-0.09983597438230.1970864594770.4235813372240.2363921376620.0694883289102-0.07454328006340.1157127550770.05525288128220.227612698909-2.8410963959425.361814151141.4416783107
284.20070951495-1.25383811474-0.5607221119911.74872473001-0.9241698274531.10781010207-0.1137276172530.53771142965-0.779549809227-0.3039024018940.1745635099940.3096123944250.723708533291-0.18322931668-0.07497152807060.4619333716340.07625171443650.01962204643930.460009296898-0.03664622318150.324253105333-8.612935760713.919004328731.0925969372
292.70568730213-0.6125158972380.552397857290.753250652777-0.5447174042560.399207907490.2176187472530.5487994696260.0047574376383-0.346887946795-0.325848581592-0.1782398079780.2129990527630.2693554869760.07232215427770.3764697290860.0983651504181-0.01826253628160.225828568380.03614512373070.131475122867-9.2924300432826.783732238130.7181715143
300.9727226503770.4703164213050.1823990110050.2540573688940.2771610823791.35094362867-0.2154905977810.1695274761110.456273715893-0.1659439601080.130343467589-0.0062961562359-0.202109649858-0.06575523477560.6118118140650.215879905134-0.0581736585531-0.1672459240240.1289743532860.06751739584880.418884091428-0.5413844482928.767877839945.5327045601
311.43440510845-1.29115733875-0.1024989997122.93768966363-0.6363894267681.43066870730.2297826416790.159161246957-0.207874555981-0.0630191147357-0.003002474836650.4554059740790.146555554323-0.2872645799930.1006244721930.1688193531150.054563112665-0.0192299516670.23792876844-0.05664907387010.14747440519-15.477300423423.299209247734.9892465448
321.90952837154-0.0785414359104-1.60837810361.63603775458-0.1810253846231.39180856041-0.2327987097090.19992418141-0.345021851978-0.249017076987-0.00118222506225-0.4522995010250.1586507735190.144800977568-0.4887047861370.2650708935820.01544803050580.2007610168750.9298790796830.05755401646110.5294058552562.8669166854820.072985820323.754703178
332.641487927080.3785408009580.5229005865172.76431804082.636213289412.525599544990.230789547556-0.286963459709-0.5330758655360.35248974540.3537458517210.3013785595150.6620701380930.2108670695180.9085478850010.1566379703970.100634244517-0.007501302485290.3971325551290.1107992867870.319979186415-5.7407531602315.382801720740.2703238603
342.138144371440.611898970290.9636595384434.839931935180.4321720931872.698632450390.1652820071920.05116533751770.3158088817320.3768099637150.4155022531191.455384052190.0420181993391-0.958640255917-0.2037406637990.309862923242-0.01896764018130.1167323295060.5175593373450.1628263239380.412631219166-20.274034010121.643069423241.3810035719
351.510847796490.529250420973-0.04585759515391.46291364080.2801183273962.74724340723-0.03988734261880.168220812897-0.2142293647480.2637364944690.1136503592160.2498285185810.225980743709-0.6666543697077.03013529728E-50.2525960851230.04734913986390.1052854239780.264973845830.1036321958320.208034065683.472011185512.07831425518-2.61978657812
360.6276506027150.7043371309610.1206620641441.04545708986-0.2437313905432.61166013624-0.0555985225961-0.273805078816-0.03150442510630.05918571380820.124047281380.253192164749-0.208940391823-0.551146707386-0.1493924928490.2907412357890.1260316392580.0696654332550.3048461614650.1142041570670.1106813060717.640737967857.00626947609-5.16222500235
374.089151895281.57870633160.5857432532412.6831647959-1.059098551931.023886577490.05189128671210.123298755285-0.667798581645-0.284746716288-0.0171228888553-0.3375232352770.6842638258910.02009324760430.2651785341990.4742156824140.09784895612810.008902408727540.1540874605630.08930747388130.20315998826312.31925162923.33483417988-16.6038789543
382.0342503668-0.09306822010520.7063163855791.384908610660.1721396736613.325031706650.0132495523777-0.281959844332-0.2011063626970.1685451635340.1485563238750.223052697979-0.226224896123-0.74264451898-0.2242882157230.2324094320060.1005864590710.007630607252430.2308551608930.1265394876380.1809676402297.977006210957.26896621948-8.84687141399
391.67256232406-1.02444774144-1.545544382232.716939779110.6731416398963.874599289970.3067542019110.127603477709-0.606598308871-0.687140963129-0.0426007664504-0.635243432360.239276827152-0.058382688393-0.1261365979280.396195893131-0.06725100162170.08065987350810.467878833868-0.01443560323440.35914905433425.39121823834.16223474266-18.4281286016
401.98101870294-1.051282722420.4556574172020.87637928222-0.09923283371283.27492737933-0.118412990866-0.302597148415-0.8948823398120.02218187495740.2396981895730.5050063030970.560295320475-0.541292199709-0.1353483621810.2422881658020.07972308922350.05352892357090.3135399256320.1467697276270.3800737410727.09849916018-1.11457516475-8.72125361225
410.249702352586-0.550687420554-0.09898318538012.16524925643-1.181409847522.09963594848-0.2148576553180.006172842978680.2446692006340.41892623808-0.0320555090759-0.33057182264-0.3034013423420.0609827588007-0.3573360380550.2078342520830.113463780908-0.02524934348150.1780295950920.0774818206250.2739428510571.0726343106421.230199750958.2880022498
420.08664244337170.0610093188174-0.1409002672890.1851407289110.1121288216460.5443586501420.00795513760065-0.01171632770820.03950771817220.01381588352460.1050196837030.06903953906210.219765206749-0.376325270902-0.4311482531430.6367685475970.223873231550.03187346504340.7657499101380.203005582910.284243955434-14.710994561119.04847847856.1625981499
431.080293127150.2197744122710.3096225789911.13407905062-0.5349609387851.683857737980.138496986141-0.119455746208-0.181028015038-0.01377472276470.1395028559480.370370766084-0.0340718612012-0.907331926780.2381320731540.2116270678930.0422037097191-0.09639580647930.6343666888470.0519483527170.243890759956-13.773292393915.611108044661.231857859
440.6995633994430.3377527940390.5790132017191.32889042805-0.1406232130930.627894676258-0.01794323392380.3066793521640.128679246239-0.305313283458-0.117602169039-0.181175705655-0.03168261085260.11549408521-0.1558008828570.2653817189730.1220531641520.03073723967420.2091954935170.1327143452420.2081715747082.5556117730214.750602623259.9648284865
453.73413974815-1.183293232580.8215341049670.376089141588-0.295429628331.31590519388-0.1531920889110.2511632449341.096513461180.2985518222090.129513732469-1.06627900022-0.748603027949-0.04526788812890.02556724907920.848850793657-0.1483994922550.06389776175590.2883222635350.003297284547290.6780560710680.81439344966724.630675194773.2656846481
461.742666065160.238227369337-0.8984331640843.57029651219-1.105559237821.514022159660.1737006437890.09076260231450.07634465068910.0165886044988-0.246664755044-0.298305035637-0.08334721565350.216903879107-0.06737948399680.2140766239340.08806582656010.03282671995720.1115316510050.04652591206470.1790332139681.4704998236111.930549702262.6629207478
472.985639912790.2861546996991.147404384431.16227824712-0.7784533258032.895431164970.0714100210693-0.4452139244540.0491238295190.3103678635620.146685944740.276551843848-0.28714824832-0.698129699865-0.2536170362950.3320146398660.05848148429420.07127415087570.3067707371840.1558632872610.197061249124-7.7388804509116.703277725769.9747517129
480.5120488840121.17358389654-0.5927464606682.70191559327-1.459156818811.445850365450.440989412749-0.03251920672211.01829655960.9942008747620.433167778862-1.37142312564-0.5961924887910.828897631472-0.3071333073440.5466086612560.0632296929836-0.08252762868150.771887000697-0.05613334249660.65115573003513.077270600216.637738717976.3066078258
490.1977117742070.0454942005719-0.04835989168440.44866281926-0.2899048446660.1896490532830.03108000770450.1447441265940.353045441712-0.250252679152-0.01745668910110.210526893712-0.326079595417-0.03317314285-0.1512413105150.543808529692-0.00685156120706-0.04741065975230.1148369005030.02853473286640.4698748971761.2063605350224.575512279163.2160273155
500.2025084866411.03964467832-0.0772820307265.43878979717-0.4466326395790.05467111855220.00256083176843-0.2788075136990.1389206224440.1786002911290.1198267611240.520369731317-0.138020250299-0.435981769264-0.7029611511430.2313870823980.231817199653-0.003982687992930.6166907497620.04435570078220.181784756612-13.785792563419.496808947265.4398509444
512.268764343270.427153322822-1.900567274211.840204301020.7054290436862.42614722233-0.1909176212160.6198694237220.0348699158018-0.00545354482507-0.0887267120721-0.115828281150.415189180517-0.34975955502-0.9968872236540.3000682967190.02091900019710.1752884033740.4183643832060.2119857703320.560294427888-30.8029901864-14.449649432143.0197721483
523.03058022568-0.1091804842620.4614856513763.18830146899-1.350243902582.936538014790.2296396929440.707206381335-0.0318012171823-0.378176857065-0.268852374663-0.182482987190.513486183115-0.714924050927-0.1110354874370.549946698498-0.1440833866390.2277937376110.5018241474610.04011084752170.359917955183-37.8140850145-20.469686665540.0397893266
530.171277539817-0.1792760053180.108842614790.263830533181-0.2925163643460.468633353465-0.1505161859850.2075557757330.143701432635-0.2969656517290.00897061620058-0.4012438803610.0001107874533670.18316298521-0.3406904641280.191529879869-0.03114452982650.1752662036750.1659135147150.1543928105730.518928728786-28.439741998-17.142781637653.0706522697
543.93129845025-1.151065422262.364509932261.63503426007-1.175782721573.011414818590.056398331597-0.3663519645850.792810754360.130759968543-0.205182846636-0.407713675444-0.389593701326-0.207230967887-0.08238547157780.161053492815-0.01050402344920.06551440071120.361832660770.1678293252270.470465785991-40.4569395743-13.403077839256.4115712203
552.504942439561.448931267630.107686443311.52773796498-0.858185098811.23252395010.00425105066031-0.0216149808251-0.4269910964550.0738540116867-0.197046529056-0.584486130955-0.2881598144780.3237112951620.4095329826950.455604668287-0.03205702440.2083532546390.2332556350810.06772881860240.536251888925-23.7820737331-20.313563639951.9122618554
563.17855057183-0.6077864537610.2454472402337.49223983307-0.2369839924921.202603561960.08086240446510.5985223183270.0448682636162-0.565485946325-0.3182897181061.021378896750.572662403364-0.7308855567380.1568359623170.517833739465-0.03303383538820.2381290876280.478564539849-0.03854544559490.527863379939-45.8932891641-18.362876149944.7388119489
571.18100048320.62805558191.04364209771.249678515090.02595873627743.72833162469-0.0534555187529-0.06774754431220.315359117690.7889531212280.0497240037921-0.0690941896666-0.463182298117-0.08714090859610.3729001317920.4441072861430.0196966985198-0.01228789943770.1276029614730.01146925666970.655355389783-34.2952051909-13.395171059162.1348901482
581.707593472120.2790948646630.3241439609953.647807291141.148943984770.394827343694-0.0699248454613-0.2767823843860.5972149605820.9079941889580.180494351276-0.0831205332711-0.581546584685-0.2487496772460.2653109098470.6176706327180.15179566962-0.04405000579840.1738152896250.007262005708120.444450629884-38.6047972097-11.014297650965.304198545
590.2468080192570.1254255741170.04068805555610.06358657363070.02078033471340.00672596549899-0.1745001703320.582156249030.4569885825460.0257445525728-0.302879214777-0.31510083816-0.3394772206570.6779653046550.002102523623970.37051133466-0.0475784598-0.1955490114470.5678454707560.3444125996340.956707681043-30.910654682-5.2240488398747.7751223003
602.99594534870.3868680962860.9922987624512.056481314530.3684445132873.38915653847-0.1781706190280.8081055690880.636309379996-0.856227930272-0.3692263253670.53185270090.123810221588-0.7016521220010.1812929477270.5355224836070.03262120099680.06967567739820.4547638904780.03560049932610.428897201254-41.4602522371-16.563729706140.8342604402
611.36953489473-0.1583283590841.258237819521.669029270530.6934437522931.5841456868-0.0234948273414-0.360237319114-0.0646147456232-0.128524220133-0.06650843841160.174044055044-0.0694512283423-0.253415793188-0.3323124707940.2561687691290.0987758542244-0.03780399209150.2238923916940.131132769740.221459485802-30.611293766437.04317090363.50722581344
621.44608130302-0.3789053741230.5022397817482.39705314358-0.7519053067532.02218607964-0.0950563171740.3367786182590.08634849955210.0567312097416-0.348448472436-0.3044463645660.4479623382310.6797796466150.2822354844270.402250743420.128462688782-0.03568223345750.3008421714430.09381255222650.237745148772-22.979094347938.0461075934-6.29409462154
630.267912583877-0.0679949906809-0.3945150933851.73763754623-0.07483097902410.5962175428350.272371727269-0.114193025551-0.765434342664-0.618092964959-0.04388656701950.3087156640990.57951298344-0.221410572992-0.2331145595320.372351493652-0.0461401786281-0.2060057645610.2440763067360.1366296038370.523376078157-34.497102003934.9328593706-12.3056178936
642.0198274889-0.3877525828550.08279969280131.87904730255-0.7237126356742.138363993340.187301887808-0.456288019562-0.319540897973-0.265984042643-0.140742609854-0.03176665357120.04856614067840.138927557308-0.02359172456170.2073205406890.0638678388199-0.0248020348290.295741280960.02610203321930.318060563804-29.991276962839.1305925509-4.77486866302
651.393511497710.1314739907680.6427981726656.17425260741.576194490373.10861872203-0.00399354627269-0.0464011502186-0.447082635345-0.7068270352710.9435087597920.1090965961790.751387517565-0.249075214102-0.5966968301821.298581470310.009935763887-0.04000947471830.7212434798130.08894394970130.43756621401-28.357407732533.3153675373-24.1566881849
660.762697183402-0.1737941873950.05537284738391.1515981612-0.7317559540351.409542483730.101082838532-0.224912777419-0.6315178037640.134087213503-0.0321732313860.06914491198040.5723260424130.1285323586730.4660374538780.6029697682050.00952398400162-0.1189472602570.1648895126370.1028144477830.380349004359-30.954327228131.1246304615-3.29542002363
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 24 through 50 )AA24 - 501 - 27
22chain 'A' and (resid 51 through 70 )AA51 - 7028 - 47
33chain 'A' and (resid 71 through 80 )AA71 - 8048 - 57
44chain 'A' and (resid 81 through 104 )AA81 - 10458 - 81
55chain 'A' and (resid 105 through 121 )AA105 - 12182 - 98
66chain 'A' and (resid 122 through 133 )AA122 - 13399 - 110
77chain 'A' and (resid 134 through 152 )AA134 - 152111 - 129
88chain 'B' and (resid 24 through 40 )BF24 - 401 - 17
99chain 'B' and (resid 41 through 51 )BF41 - 5118 - 28
1010chain 'B' and (resid 52 through 59 )BF52 - 5929 - 36
1111chain 'B' and (resid 60 through 70 )BF60 - 7037 - 47
1212chain 'B' and (resid 71 through 80 )BF71 - 8048 - 57
1313chain 'B' and (resid 81 through 90 )BF81 - 9058 - 67
1414chain 'B' and (resid 91 through 103 )BF91 - 10368 - 80
1515chain 'B' and (resid 104 through 121 )BF104 - 12181 - 98
1616chain 'B' and (resid 122 through 133 )BF122 - 13399 - 110
1717chain 'B' and (resid 134 through 141 )BF134 - 141111 - 118
1818chain 'B' and (resid 142 through 153 )BF142 - 153119 - 130
1919chain 'C' and (resid 25 through 70 )CG25 - 701 - 46
2020chain 'C' and (resid 71 through 80 )CG71 - 8047 - 56
2121chain 'C' and (resid 81 through 90 )CG81 - 9057 - 66
2222chain 'C' and (resid 91 through 121 )CG91 - 12167 - 97
2323chain 'C' and (resid 122 through 133 )CG122 - 13398 - 109
2424chain 'C' and (resid 134 through 153 )CG134 - 153110 - 129
2525chain 'D' and (resid 25 through 40 )DK25 - 401 - 16
2626chain 'D' and (resid 41 through 51 )DK41 - 5117 - 27
2727chain 'D' and (resid 52 through 70 )DK52 - 7028 - 46
2828chain 'D' and (resid 71 through 80 )DK71 - 8047 - 56
2929chain 'D' and (resid 81 through 90 )DK81 - 9057 - 66
3030chain 'D' and (resid 91 through 103 )DK91 - 10367 - 79
3131chain 'D' and (resid 104 through 121 )DK104 - 12180 - 97
3232chain 'D' and (resid 122 through 133 )DK122 - 13398 - 109
3333chain 'D' and (resid 134 through 146 )DK134 - 146110 - 122
3434chain 'D' and (resid 147 through 152 )DK147 - 152123 - 128
3535chain 'E' and (resid 25 through 40 )EO25 - 401 - 16
3636chain 'E' and (resid 41 through 70 )EO41 - 7017 - 46
3737chain 'E' and (resid 71 through 90 )EO71 - 9047 - 66
3838chain 'E' and (resid 91 through 121 )EO91 - 12167 - 97
3939chain 'E' and (resid 122 through 133 )EO122 - 13398 - 109
4040chain 'E' and (resid 134 through 152 )EO134 - 152110 - 128
4141chain 'F' and (resid 25 through 33 )FR25 - 331 - 9
4242chain 'F' and (resid 34 through 40 )FR34 - 4010 - 16
4343chain 'F' and (resid 41 through 51 )FR41 - 5117 - 27
4444chain 'F' and (resid 52 through 70 )FR52 - 7028 - 46
4545chain 'F' and (resid 71 through 80 )FR71 - 8047 - 56
4646chain 'F' and (resid 81 through 103 )FR81 - 10357 - 79
4747chain 'F' and (resid 104 through 121 )FR104 - 12180 - 97
4848chain 'F' and (resid 122 through 133 )FR122 - 13398 - 109
4949chain 'F' and (resid 134 through 146 )FR134 - 146110 - 122
5050chain 'F' and (resid 147 through 152 )FR147 - 152123 - 128
5151chain 'H' and (resid 25 through 40 )HT25 - 401 - 16
5252chain 'H' and (resid 41 through 51 )HT41 - 5117 - 27
5353chain 'H' and (resid 52 through 70 )HT52 - 7028 - 46
5454chain 'H' and (resid 71 through 90 )HT71 - 9047 - 66
5555chain 'H' and (resid 91 through 103 )HT91 - 10367 - 79
5656chain 'H' and (resid 104 through 115 )HT104 - 11580 - 91
5757chain 'H' and (resid 116 through 127 )HT116 - 12792 - 103
5858chain 'H' and (resid 128 through 136 )HT128 - 136104 - 112
5959chain 'H' and (resid 137 through 146 )HT137 - 146113 - 122
6060chain 'H' and (resid 147 through 152 )HT147 - 152123 - 128
6161chain 'G' and (resid 25 through 51 )GX25 - 511 - 27
6262chain 'G' and (resid 52 through 70 )GX52 - 7028 - 46
6363chain 'G' and (resid 71 through 90 )GX71 - 9047 - 66
6464chain 'G' and (resid 91 through 121 )GX91 - 12167 - 97
6565chain 'G' and (resid 122 through 133 )GX122 - 13398 - 109
6666chain 'G' and (resid 134 through 152 )GX134 - 152110 - 128

+
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