[English] 日本語
Yorodumi
- PDB-6kam: Crystal structure of FKRP in complex with Ba ion, CDP-ribtol, and... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kam
TitleCrystal structure of FKRP in complex with Ba ion, CDP-ribtol, and sugar acceptor
ComponentsFukutin-related protein
KeywordsTRANSFERASE / glycosyltranferase / phospho ribitoyl tranferase
Function / homology
Function and homology information


pentitol metabolic process / filtration diaphragm assembly / pentose metabolic process / connective tissue development / creatine metabolic process / connective tissue replacement / Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / oxygen metabolic process / phosphotransferase activity, for other substituted phosphate groups / localization of cell ...pentitol metabolic process / filtration diaphragm assembly / pentose metabolic process / connective tissue development / creatine metabolic process / connective tissue replacement / Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / oxygen metabolic process / phosphotransferase activity, for other substituted phosphate groups / localization of cell / diaphragm development / maintenance of protein localization in endoplasmic reticulum / protein O-linked glycosylation via mannose / skeletal muscle fiber differentiation / basement membrane organization / dystroglycan binding / glial cell differentiation / reelin-mediated signaling pathway / skeletal muscle tissue regeneration / respiratory system process / protein import / camera-type eye development / response to alcohol / adult walking behavior / neuromuscular process / bone mineralization / skeletal muscle myofibril / heart morphogenesis / laminin binding / rough endoplasmic reticulum / response to glucocorticoid / muscle contraction / glycolytic process / response to activity / protein tetramerization / phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein processing / sarcolemma / brain development / lipid metabolic process / neuron migration / in utero embryonic development / response to xenobiotic stimulus / inflammatory response / Golgi membrane / Golgi apparatus / extracellular space / nucleoplasm / metal ion binding / identical protein binding / cytosol
Similarity search - Function
LicD family / : / : / LicD family / Fukutin-related protein stem domain
Similarity search - Domain/homology
: / CYTIDINE-5'-DIPHOSPHATE / PHOSPHATE ION / D-ribitol / Ribitol 5-phosphate transferase FKRP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsKuwabara, N.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16K07284 Japan
Japan Society for the Promotion of Science26840029 Japan
CitationJournal: Nat Commun / Year: 2020
Title: Crystal structures of fukutin-related protein (FKRP), a ribitol-phosphate transferase related to muscular dystrophy.
Authors: Kuwabara, N. / Imae, R. / Manya, H. / Tanaka, T. / Mizuno, M. / Tsumoto, H. / Kanagawa, M. / Kobayashi, K. / Toda, T. / Senda, T. / Endo, T. / Kato, R.
History
DepositionJun 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fukutin-related protein
B: Fukutin-related protein
C: Fukutin-related protein
D: Fukutin-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,46430
Polymers200,1074
Non-polymers5,35726
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16500 Å2
ΔGint-99 kcal/mol
Surface area74040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.571, 119.240, 254.646
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Fukutin-related protein / Ribitol-5-phosphate transferase


Mass: 50026.805 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKRP / Cell line (production host): HEK293S GnT- / Production host: Homo sapiens (human) / References: UniProt: Q9H9S5

-
Sugars , 2 types, 8 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)- ...2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpNAcb1-3DGlcpNAcb1-4DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GalpNAc]{}}}LINUCSPDB-CARE
#4: 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.: 7
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

-
Non-polymers , 6 types, 211 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE


Mass: 403.176 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H15N3O11P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-RB0 / D-ribitol


Mass: 152.146 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C5H12O5 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ba / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 4-8 % PEG 4,000, 0.1 M HEPES-NaOH (pH7.5), 0.5 M LiCl2 and 20 mM BaCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.46→45.69 Å / Num. obs: 86984 / % possible obs: 99.76 % / Redundancy: 6.5 % / Biso Wilson estimate: 55.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.051 / Rrim(I) all: 0.095 / Net I/σ(I): 19.8
Reflection shellResolution: 2.46→2.51 Å / Rmerge(I) obs: 1.315 / Num. unique obs: 8055 / CC1/2: 0.745 / Rpim(I) all: 0.759 / Rrim(I) all: 1.424

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→45.69 Å / SU ML: 0.3515 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2135 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2492 4332 4.98 %
Rwork0.2084 82652 -
obs0.2104 86984 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.35 Å2
Refinement stepCycle: LAST / Resolution: 2.46→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13769 0 290 193 14252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007314498
X-RAY DIFFRACTIONf_angle_d0.948819896
X-RAY DIFFRACTIONf_chiral_restr0.0512222
X-RAY DIFFRACTIONf_plane_restr0.0062601
X-RAY DIFFRACTIONf_dihedral_angle_d7.535910083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.490.36051250.35322608X-RAY DIFFRACTION95.93
2.49-2.520.39061500.36182706X-RAY DIFFRACTION99.93
2.52-2.550.37561360.35542741X-RAY DIFFRACTION99.86
2.55-2.590.36451520.33122706X-RAY DIFFRACTION99.97
2.59-2.620.37971530.33932728X-RAY DIFFRACTION99.9
2.62-2.660.37071410.31992710X-RAY DIFFRACTION99.96
2.66-2.690.39141350.31352747X-RAY DIFFRACTION99.83
2.69-2.730.34121520.29262708X-RAY DIFFRACTION99.83
2.73-2.780.29521420.27562734X-RAY DIFFRACTION99.93
2.78-2.820.30891480.26442723X-RAY DIFFRACTION99.76
2.82-2.870.35931400.26072736X-RAY DIFFRACTION99.97
2.87-2.920.3071450.26192745X-RAY DIFFRACTION99.97
2.92-2.980.29111310.26682729X-RAY DIFFRACTION99.79
2.98-3.040.30471540.26862759X-RAY DIFFRACTION99.93
3.04-3.110.30671480.26432733X-RAY DIFFRACTION100
3.11-3.180.29031450.2512723X-RAY DIFFRACTION99.83
3.18-3.260.31681460.2522748X-RAY DIFFRACTION99.9
3.26-3.350.2841400.23162736X-RAY DIFFRACTION99.83
3.35-3.440.26161550.23042727X-RAY DIFFRACTION99.93
3.44-3.550.26751450.22112775X-RAY DIFFRACTION99.97
3.55-3.680.2491500.2132730X-RAY DIFFRACTION99.93
3.68-3.830.24441400.19482785X-RAY DIFFRACTION99.8
3.83-40.22581510.17752742X-RAY DIFFRACTION99.93
4-4.210.21591420.17562793X-RAY DIFFRACTION99.9
4.21-4.480.21711230.16312816X-RAY DIFFRACTION99.9
4.48-4.820.20051530.15572771X-RAY DIFFRACTION99.97
4.82-5.310.18561330.16232835X-RAY DIFFRACTION99.93
5.31-6.070.22081450.19252821X-RAY DIFFRACTION99.97
6.07-7.650.20711670.1772839X-RAY DIFFRACTION100
7.65-45.690.19171450.16152998X-RAY DIFFRACTION99.43
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)
12.050003112990.9385700332030.1263765290972.658426147720.4707002882243.31022840651-0.0286894503833-0.04473672223420.2094205879260.0171292597956-0.07481136262980.432358743147-0.389085353081-0.5012632671560.1186311829560.6247115148610.140418413922-0.007524526945240.4512873361930.01308969764970.424845203445-8.08811531963243.09898834.9542353443
24.248303780421.094145114412.886516051231.402911352511.467252727482.329105950780.054108268857-0.103248130777-0.1439739675670.4641518530370.0325205675359-0.1946414888680.0222501134586-0.14724123201-0.03997848346260.7273757706750.01931935591960.0005568028829860.4428318799380.05392256955550.36168958260715.3068902174238.21250691751.7127235758
34.92371243679-0.3750149552721.980814976155.668165644771.157393853495.2639650022-0.1644862573580.05482169993210.3786742001230.6715553412140.165556309292-1.07184363216-0.01213845335650.58271722703-0.005769351192120.6949617934380.00569296100061-0.2039457569070.5017848366450.04206713082690.65983066735834.154726354246.33899091864.6087453166
44.477701728551.64940694030.4341285089856.116789020060.7232298231023.30453111606-0.1512010841860.0959559521763-0.0543261004654-0.1398217188710.227861732469-1.18816111631-0.3450557744680.434035686581-0.2148077470790.676040247757-0.0961074187220.04301902224360.439750240581-0.06409035069210.66601985358629.7678269497251.42775873422.4695199879
52.5228415140.9733025083060.6488232181073.022253740360.7959352769552.37429475070.313061993306-0.469965630841-0.124189450621-0.00341117258629-0.372855735898-0.384158467403-0.07073875412330.0905632819264-0.04757200410570.649552856137-0.0579418529325-0.03415723682710.4399375417960.04107794207310.52866148413121.8201329802251.44735022332.8858403467
63.032780793221.035496716520.3238556357033.871762196811.251296902293.52457424361-0.0167750053420.5219384893960.0916035689679-0.8023824035780.276210971645-0.682284818704-0.581422523820.437696591352-0.1128083297640.871766934892-0.1348866654420.1686561061940.468973043885-0.01487692883340.62631615741424.3936068519252.18442412814.3205097979
73.323249454562.13575845530.686311804053.694647048471.214111350072.05551450189-0.05404443866750.53795060879-0.630057719098-0.4220418265890.305903191699-0.795418684567-0.07409735280210.311115099043-0.247676027250.7521368603180.0001919041701130.1204430038710.450733449233-0.09220885332150.62701255872623.5825946913237.96901813111.5688741679
81.476032873882.6460580171.355171108164.830236205322.102398372981.031007509750.565599567861-0.206637956672-0.6036658758130.0901414808086-0.0716033222249-1.59730874707-0.1433235704320.309971147686-0.2907809746180.7428630054410.0213225465667-0.1608563010530.514319799915-0.01591105638790.97068603432220.2446012148223.56278892122.0825726982
92.21959632882-0.2850078654760.2696535438756.070601444070.348193740542.648847736220.137489693174-0.25699951203-0.2625541636650.319746257991-0.0676467631665-0.09633992005850.428021049568-0.256066719426-0.06836370139410.48625157673-0.0445589172546-0.0761672450030.3647316246070.05998846868380.412343076350.177777070526201.99870822516.0602171327
101.917933026140.132426315048-0.4799602934421.78294780421-0.2651004155471.64194419083-0.101335803973-0.227603695715-0.1600888949820.0895750032632-0.115894219833-0.3811878672170.2718219700790.3399276747560.2093366398930.6601332339690.0468605228337-0.06269214699340.4768054445660.06710940334110.50308797652644.6979829783278.66922349237.4404515275
112.82461537327-0.714377992529-2.287439991612.14264392643-0.1424478907795.2226158289-0.007066493391190.03846967622310.01119190970190.32528695103-0.1032358470410.559833685901-0.545234843015-0.6144703856990.1496861846920.7600181844650.05162163243870.07532864516050.496952330967-0.0855534679370.5229009445246.61577438002277.42455810563.1548563404
121.0380734172-0.742863717642-0.6632858264480.928207476321.302688514287.45510776646-0.4344782481080.010104520802-0.7155742346960.129668267592-0.07941369457990.8354430700880.977379529531-0.5220760551880.5456991071050.944802021696-0.0615539794250.1676659760730.665768110512-0.05666690633610.865308637859.24378472573262.88145861563.1507489735
131.866001778290.917479687216-0.1618784403832.79483556391-0.4028200159941.3714060795-0.1150367337990.2552150341670.07818849605-0.4111306322290.1338788139630.3176727230830.00159515497021-0.14827543727-0.01400298568350.683077682082-0.0134608272688-0.0760501242280.404098068268-0.006040432981940.38833153621512.9694368478277.87919907619.6615151234
142.226416411360.729965195283-0.3309913091293.56577786798-1.169204123792.312635050960.335280509268-0.3377226030570.2941149084210.299689915121-0.310934184041-0.182259437934-0.609527506140.489089505082-0.0177587012520.703037529816-0.149297122560.009557788601320.473109735659-0.00899702465650.39869258263335.485481154317.33806056720.0410250465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 46 through 250 )
2X-RAY DIFFRACTION2chain 'A' and (resid 251 through 336 )
3X-RAY DIFFRACTION3chain 'A' and (resid 337 through 491 )
4X-RAY DIFFRACTION4chain 'B' and (resid 47 through 83 )
5X-RAY DIFFRACTION5chain 'B' and (resid 84 through 111 )
6X-RAY DIFFRACTION6chain 'B' and (resid 112 through 150 )
7X-RAY DIFFRACTION7chain 'B' and (resid 151 through 253 )
8X-RAY DIFFRACTION8chain 'B' and (resid 254 through 296 )
9X-RAY DIFFRACTION9chain 'B' and (resid 297 through 491 )
10X-RAY DIFFRACTION10chain 'C' and (resid 47 through 289 )
11X-RAY DIFFRACTION11chain 'C' and (resid 290 through 454 )
12X-RAY DIFFRACTION12chain 'C' and (resid 455 through 491 )
13X-RAY DIFFRACTION13chain 'D' and (resid 47 through 271 )
14X-RAY DIFFRACTION14chain 'D' and (resid 272 through 491 )

+
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