[English] 日本語
Yorodumi
- PDB-6kal: Crystal structure of FKRP in complex with Mg ion and CMP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kal
TitleCrystal structure of FKRP in complex with Mg ion and CMP
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 / connective tissue replacement / creatine metabolic process / Matriglycan biosynthesis on DAG1 / oxygen metabolic process / Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / phosphotransferase activity, for other substituted phosphate groups ...pentitol metabolic process / filtration diaphragm assembly / pentose metabolic process / connective tissue development / connective tissue replacement / creatine metabolic process / Matriglycan biosynthesis on DAG1 / oxygen metabolic process / Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / 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 / reelin-mediated signaling pathway / glial cell differentiation / respiratory system process / skeletal muscle tissue regeneration / protein import / camera-type eye development / adult walking behavior / response to alcohol / neuromuscular process / bone mineralization / skeletal muscle myofibril / heart morphogenesis / rough endoplasmic reticulum / laminin binding / response to glucocorticoid / muscle contraction / response to activity / glycolytic process / lipid metabolic process / phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein tetramerization / protein processing / brain development / sarcolemma / neuron migration / in utero embryonic development / response to xenobiotic stimulus / inflammatory response / Golgi membrane / Golgi apparatus / : / 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'-MONOPHOSPHATE / Ribitol 5-phosphate transferase FKRP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 6, 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)203,40527
Polymers200,1074
Non-polymers3,29723
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14680 Å2
ΔGint-128 kcal/mol
Surface area73580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.583, 118.674, 252.695
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Sugars , 2 types, 11 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
#3: 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
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 , 4 types, 275 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.91 Å3/Da / Density % sol: 57.68 %
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) and 0.2 M MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→48.9962 Å / Num. obs: 72606 / % possible obs: 99.93 % / Redundancy: 6.7 % / Net I/σ(I): 13.56
Reflection shellResolution: 2.6→2.6342 Å / Num. unique obs: 2628

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→48.987 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.04
RfactorNum. reflection% reflection
Rfree0.2409 3680 5.07 %
Rwork0.1947 --
obs0.1971 72606 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→48.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13701 0 194 259 14154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114317
X-RAY DIFFRACTIONf_angle_d1.00219635
X-RAY DIFFRACTIONf_dihedral_angle_d7.4089991
X-RAY DIFFRACTIONf_chiral_restr0.0562187
X-RAY DIFFRACTIONf_plane_restr0.0092582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.63420.38161360.332628X-RAY DIFFRACTION100
2.6342-2.67030.33661420.32632601X-RAY DIFFRACTION100
2.6703-2.70840.34631330.29842601X-RAY DIFFRACTION100
2.7084-2.74890.33881490.2762619X-RAY DIFFRACTION100
2.7489-2.79180.32021360.26282618X-RAY DIFFRACTION100
2.7918-2.83760.32871480.26032624X-RAY DIFFRACTION100
2.8376-2.88650.34271270.2592617X-RAY DIFFRACTION100
2.8865-2.9390.32331480.25762619X-RAY DIFFRACTION100
2.939-2.99550.27721360.2562627X-RAY DIFFRACTION100
2.9955-3.05660.34111380.25292622X-RAY DIFFRACTION100
3.0566-3.12310.28981290.23552653X-RAY DIFFRACTION100
3.1231-3.19570.2851450.23252610X-RAY DIFFRACTION100
3.1957-3.27560.2641470.22232607X-RAY DIFFRACTION100
3.2756-3.36420.28121550.21162660X-RAY DIFFRACTION100
3.3642-3.46320.25451330.21032614X-RAY DIFFRACTION100
3.4632-3.57490.25881300.20732663X-RAY DIFFRACTION100
3.5749-3.70260.21971420.19762651X-RAY DIFFRACTION100
3.7026-3.85080.23491580.18082643X-RAY DIFFRACTION100
3.8508-4.0260.20871230.17022653X-RAY DIFFRACTION100
4.026-4.23820.23881570.16212648X-RAY DIFFRACTION100
4.2382-4.50350.19271420.15112657X-RAY DIFFRACTION100
4.5035-4.85090.17791360.14462704X-RAY DIFFRACTION100
4.8509-5.33860.18561610.16042654X-RAY DIFFRACTION100
5.3386-6.10980.23241400.17892716X-RAY DIFFRACTION100
6.1098-7.69290.19611500.17372742X-RAY DIFFRACTION100
7.6929-48.99620.19031390.16142875X-RAY DIFFRACTION99
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)
11.86810.98010.39432.01840.02662.3611-0.0455-0.08660.3167-0.0562-0.05570.4037-0.3925-0.55420.10650.56530.1376-0.00910.4527-0.01010.4435-8.0727241.915334.6439
23.61860.61772.41640.83881.21252.21120.0719-0.2214-0.12070.3163-0.0228-0.16150.0883-0.1422-0.03560.54180.04510.010.36040.04110.358515.3817236.890251.0235
35.2262-1.08812.87734.51441.00016.6635-0.0705-0.01170.27680.62340.186-1.12950.30571.0131-0.0680.58450.0274-0.10920.5260.02450.589535.7104241.584164.916
41.6702-0.3815-0.8471.1895-0.92255.5325-0.18680.17290.7658-0.07160.0218-0.7871-0.52410.3090.12530.8244-0.0953-0.12790.53260.03420.99328.8282255.944561.3593
51.98060.89580.44232.99720.36771.85640.04490.2687-0.1723-0.37250.1373-0.5535-0.1440.3014-0.14410.57480.0050.09970.3941-0.03040.490924.3801242.529617.4334
61.74050.44350.07396.03680.0132.92580.044-0.2079-0.19580.2512-0.0423-0.02440.2127-0.23030.01360.3530.015-0.04780.34390.03850.36332.0476202.979416.1555
71.63710.4563-0.51182.0673-0.06581.9765-0.0753-0.1955-0.13220.0552-0.1217-0.410.25370.44180.18240.48060.0609-0.03220.41540.07780.412744.1238277.363237.3283
82.2982-0.7418-1.70583.9157-0.09183.98930.0213-0.1029-0.08310.3757-0.06250.6363-0.1381-0.37060.0370.5403-0.03160.0330.4319-0.06480.41877.0161273.532563.03
92.70130.4637-0.2114.0585-0.31722.3803-0.12780.1273-0.1999-0.3120.20990.3770.4692-0.2505-0.07740.6366-0.0364-0.04640.36340.02680.38937.8611268.891823.5944
100.7798-0.08880.00111.5836-0.39541.263-0.04190.0163-0.08580.0199-0.0049-0.03270.0684-0.00280.03070.5338-0.0528-0.01420.312-0.04980.406416.3943267.992433.164
111.5201-0.4477-0.51062.6665-0.78331.6662-0.12980.6385-0.2486-0.41590.0310.20150.3912-0.11490.00180.7173-0.0261-0.04970.382-0.02440.345714.4091268.758219.3493
122.34921.1922-0.17942.9886-0.6781.3103-0.13840.30220.1267-0.56370.18840.40860.0127-0.1435-0.05430.65830.004-0.10540.41450.05120.413613.2345282.48815.2491
132.71150.7885-0.72883.3423-0.78462.1740.2626-0.2492-0.04830.0559-0.19830.0318-0.0510.1706-0.01040.48770.0042-0.03650.31810.02220.32228.6603300.555721.6083
142.63791.0718-0.60713.5908-0.83083.05810.3669-0.57010.41320.8047-0.2698-0.1413-0.80940.5539-0.12790.6788-0.1590.00170.4691-0.04040.411533.922320.530924.3312
152.89621.4755-0.39553.8049-0.4953.24860.0669-0.20520.22670.3858-0.1751-0.8457-0.77440.90840.03570.8271-0.21070.04040.5795-0.04380.692643.0902324.741315.0621
161.7277-0.76830.53014.8761-2.47733.06790.1460.10350.0172-0.511-0.4668-0.73460.1150.72940.35680.4889-0.01030.08520.45170.06460.450440.4845315.18578.9295
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 454 )
4X-RAY DIFFRACTION4chain 'A' and (resid 455 through 492 )
5X-RAY DIFFRACTION5chain 'B' and (resid 47 through 272 )
6X-RAY DIFFRACTION6chain 'B' and (resid 273 through 491 )
7X-RAY DIFFRACTION7chain 'C' and (resid 47 through 289 )
8X-RAY DIFFRACTION8chain 'C' and (resid 290 through 492 )
9X-RAY DIFFRACTION9chain 'D' and (resid 47 through 83 )
10X-RAY DIFFRACTION10chain 'D' and (resid 84 through 111 )
11X-RAY DIFFRACTION11chain 'D' and (resid 112 through 139 )
12X-RAY DIFFRACTION12chain 'D' and (resid 140 through 272 )
13X-RAY DIFFRACTION13chain 'D' and (resid 273 through 315 )
14X-RAY DIFFRACTION14chain 'D' and (resid 316 through 428 )
15X-RAY DIFFRACTION15chain 'D' and (resid 429 through 454 )
16X-RAY DIFFRACTION16chain 'D' and (resid 455 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