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- PDB-6fwz: Crystal structure of human UDP-N-acetylglucosamine-dolichyl-phosp... -

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Basic information

Entry
Database: PDB / ID: 6fwz
TitleCrystal structure of human UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase (DPAGT1) (V264G mutant) in complex with UDP-GlcNAc
ComponentsUDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
KeywordsTRANSFERASE / Protein glycosylation / integral membrane protein / PNPT / congenital myasthenic syndrome / antibiotic / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein / Defective DPAGT1 causes CDG-1j, CMSTA2 / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity / UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity / dolichol-linked oligosaccharide biosynthetic process / UDP-N-acetylglucosamine metabolic process / protein N-linked glycosylation / glycosyltransferase activity / intracellular membrane-bounded organelle ...Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein / Defective DPAGT1 causes CDG-1j, CMSTA2 / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity / UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity / dolichol-linked oligosaccharide biosynthetic process / UDP-N-acetylglucosamine metabolic process / protein N-linked glycosylation / glycosyltransferase activity / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / identical protein binding / membrane / metal ion binding
Similarity search - Function
: / DPAGT1 insertion domain / UDP-GlcNAc-dolichyl-phosphate GlcNAc phosphotransferase / Glycosyl transferase, family 4 / Glycosyl transferase family 4
Similarity search - Domain/homology
Chem-P6L / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Unknown ligand / UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPike, A.C.W. / Dong, Y.Y. / Chu, A. / Tessitore, A. / Goubin, S. / Dong, L. / Mukhopadhyay, S. / Mahajan, P. / Chalk, R. / Berridge, G. ...Pike, A.C.W. / Dong, Y.Y. / Chu, A. / Tessitore, A. / Goubin, S. / Dong, L. / Mukhopadhyay, S. / Mahajan, P. / Chalk, R. / Berridge, G. / Wang, D. / Kupinska, K. / Belaya, K. / Beeson, D. / Burgess-Brown, N. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Carpenter, E.P. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust106169/Z/14/Z United Kingdom
CitationJournal: Cell / Year: 2018
Title: Structures of DPAGT1 Explain Glycosylation Disease Mechanisms and Advance TB Antibiotic Design.
Authors: Dong, Y.Y. / Wang, H. / Pike, A.C.W. / Cochrane, S.A. / Hamedzadeh, S. / Wyszynski, F.J. / Bushell, S.R. / Royer, S.F. / Widdick, D.A. / Sajid, A. / Boshoff, H.I. / Park, Y. / Lucas, R. / ...Authors: Dong, Y.Y. / Wang, H. / Pike, A.C.W. / Cochrane, S.A. / Hamedzadeh, S. / Wyszynski, F.J. / Bushell, S.R. / Royer, S.F. / Widdick, D.A. / Sajid, A. / Boshoff, H.I. / Park, Y. / Lucas, R. / Liu, W.M. / Lee, S.S. / Machida, T. / Minall, L. / Mehmood, S. / Belaya, K. / Liu, W.W. / Chu, A. / Shrestha, L. / Mukhopadhyay, S.M.M. / Strain-Damerell, C. / Chalk, R. / Burgess-Brown, N.A. / Bibb, M.J. / Barry Iii, C.E. / Robinson, C.V. / Beeson, D. / Davis, B.G. / Carpenter, E.P.
History
DepositionMar 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5525
Polymers46,1741
Non-polymers1,3794
Water34219
1
A: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
hetero molecules

A: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,10510
Polymers92,3472
Non-polymers2,7578
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area7460 Å2
ΔGint-93 kcal/mol
Surface area30200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.459, 102.459, 238.209
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase / GlcNAc-1-P transferase / GPT / N-acetylglucosamine-1-phosphate transferase


Mass: 46173.719 Da / Num. of mol.: 1 / Mutation: V264G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPAGT1, DPAGT2 / Plasmid: PFB-LIC-BSE / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9H3H5, UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase

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Non-polymers , 5 types, 23 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#5: Chemical ChemComp-P6L / (2S)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6E)-HEXADEC-6-ENOYLOXY]PROPYL (8E)-OCTADEC-8-ENOATE


Mass: 746.991 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H75O10P / Comment: phospholipid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.91 Å3/Da / Density % sol: 68.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1M bicine pH 9.0 -- 0.05M sodium chloride -- 37.5% PEG300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.1→59.55 Å / Num. obs: 14197 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 85.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.033 / Rrim(I) all: 0.101 / Net I/σ(I): 14.4
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 9.9 % / Rmerge(I) obs: 2.376 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1002 / CC1/2: 0.387 / Rpim(I) all: 0.784 / Rrim(I) all: 2.505 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSOctober 15, 2015data reduction
Aimless0.5.15data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LEV

5lev


Resolution: 3.1→30 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.937 / SU B: 38.277 / SU ML: 0.314 / SU R Cruickshank DPI: 1.027 / Cross valid method: THROUGHOUT / ESU R: 1.027 / ESU R Free: 0.353 / SU Rfree Cruickshank DPI: 0.3529
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REFINED WITH AUTOBUSTER AND REFMAC IN FINAL CYCLE TO OPTIMISE UD1 GEOMETRY. PROSMART HBOND RESTRAINTS. SINGLE TLS GROUP FOR ENTIRE PROTEIN CHAIN
RfactorNum. reflection% reflectionSelection details
Rfree0.23624 728 5.2 %RANDOM
Rwork0.22257 ---
obs0.22327 13395 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 128.475 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å20 Å2
3----0.79 Å2
Refinement stepCycle: 1 / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 0 87 19 2998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193051
X-RAY DIFFRACTIONr_bond_other_d0.0020.022886
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.9744149
X-RAY DIFFRACTIONr_angle_other_deg1.01836651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8845370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76623.274113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47415464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.324159
X-RAY DIFFRACTIONr_chiral_restr0.0790.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213277
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02644
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9688.0811489
X-RAY DIFFRACTIONr_mcbond_other2.9688.0821488
X-RAY DIFFRACTIONr_mcangle_it4.66912.1241856
X-RAY DIFFRACTIONr_mcangle_other4.66812.1231857
X-RAY DIFFRACTIONr_scbond_it3.5998.6191562
X-RAY DIFFRACTIONr_scbond_other3.5998.6211563
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.62912.7742294
X-RAY DIFFRACTIONr_long_range_B_refined9.14712716
X-RAY DIFFRACTIONr_long_range_B_other9.14812717
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 49 -
Rwork0.336 947 -
obs--99.9 %
Refinement TLS params.Method: refined / Origin x: 46.141 Å / Origin y: 49.5185 Å / Origin z: 127.6888 Å
111213212223313233
T0.0717 Å2-0.0819 Å20.0058 Å2-0.5389 Å20.1616 Å2--0.1843 Å2
L4.3382 °21.1225 °2-0.8347 °2-5.8768 °2-0.2781 °2--3.3052 °2
S-0.1972 Å °0.6136 Å °0.5831 Å °-0.2193 Å °0.2897 Å °-0.4995 Å °-0.3603 Å °0.6146 Å °-0.0925 Å °

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