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- PDB-7e9l: Crystal Structure of POMGNT2 in complex with UDP and mono-mannosy... -

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Basic information

Entry
Database: PDB / ID: 7e9l
TitleCrystal Structure of POMGNT2 in complex with UDP and mono-mannosyl peptide (379Man short peptide)
Components
  • Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
  • mono-mannosyl peptide (379Man short peptide)
KeywordsTRANSFERASE / Glycosyltransferase / O-mannose type glycosylation
Function / homology
Function and homology information


O-linked glycosylation / protein O-mannose beta-1,4-N-acetylglucosaminyltransferase / protein O-linked mannosylation / protein O-acetylglucosaminyltransferase activity / acetylglucosaminyltransferase activity / protein O-linked glycosylation / neuron migration / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Glycosyltransferase 61 / : / Glycosyltransferase 61 / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
alpha-D-mannopyranose / URIDINE-5'-DIPHOSPHATE / Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKuwabara, N.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP16K07284 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101083 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05648 Japan
Japan Society for the Promotion of Science (JSPS)JP17H03987 Japan
CitationJournal: Genes Cells / Year: 2021
Title: The structure of POMGNT2 provides new insights into the mechanism to determine the functional O-mannosylation site on alpha-dystroglycan.
Authors: Imae, R. / Kuwabara, N. / Manya, H. / Tanaka, T. / Tsuyuguchi, M. / Mizuno, M. / Endo, T. / Kato, R.
History
DepositionMar 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
B: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
C: mono-mannosyl peptide (379Man short peptide)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,10213
Polymers124,4613
Non-polymers2,64110
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11840 Å2
ΔGint-17 kcal/mol
Surface area44540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.394, 104.440, 126.836
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 / POMGnT2 / Extracellular O-linked N-acetylglucosamine transferase-like / Glycosyltransferase-like ...POMGnT2 / Extracellular O-linked N-acetylglucosamine transferase-like / Glycosyltransferase-like domain-containing protein 2


Mass: 61563.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: POMGNT2, AGO61, GTDC2 / Production host: Homo sapiens (human)
References: UniProt: Q5NDF2, protein O-mannose beta-1,4-N-acetylglucosaminyltransferase
#2: Protein/peptide mono-mannosyl peptide (379Man short peptide)


Mass: 1333.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Sugars , 3 types, 7 molecules

#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.: 1
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: 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: obtained synthetically / 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
#7: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 468 molecules

#5: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl (pH 8.0 or 8.5), 12-16% PEG 8000, 1% tacsimate (pH 7.0)
PH range: 8.0 - 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.29 Å / Num. obs: 72133 / % possible obs: 99.8 % / Redundancy: 13.9 % / Biso Wilson estimate: 37.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.032 / Net I/σ(I): 16
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 1.574 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4284 / CC1/2: 0.791 / Rpim(I) all: 0.424

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1300018733

Resolution: 2.1→48.29 Å / SU ML: 0.2412 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1191
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2338 3481 4.83 %
Rwork0.1855 68574 -
obs0.1878 72055 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.08 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8414 0 167 465 9046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00768838
X-RAY DIFFRACTIONf_angle_d0.876512072
X-RAY DIFFRACTIONf_chiral_restr0.05531360
X-RAY DIFFRACTIONf_plane_restr0.00591532
X-RAY DIFFRACTIONf_dihedral_angle_d17.61791201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.33931260.2792570X-RAY DIFFRACTION95.03
2.13-2.160.29461260.26272718X-RAY DIFFRACTION99.72
2.16-2.190.29311380.23422735X-RAY DIFFRACTION99.65
2.19-2.230.33011320.23532705X-RAY DIFFRACTION99.75
2.23-2.260.28291230.23342723X-RAY DIFFRACTION99.96
2.26-2.30.24531320.22552709X-RAY DIFFRACTION99.79
2.3-2.340.25241780.21542653X-RAY DIFFRACTION99.82
2.34-2.390.28191590.21232731X-RAY DIFFRACTION99.86
2.39-2.440.27781460.20252724X-RAY DIFFRACTION99.9
2.44-2.490.26111450.19892740X-RAY DIFFRACTION99.93
2.49-2.550.26591310.20272718X-RAY DIFFRACTION99.96
2.55-2.610.24521280.20292724X-RAY DIFFRACTION99.96
2.61-2.680.26271150.20142746X-RAY DIFFRACTION100
2.68-2.760.2661300.20032743X-RAY DIFFRACTION100
2.76-2.850.23261490.19312730X-RAY DIFFRACTION100
2.85-2.950.2391500.19712737X-RAY DIFFRACTION100
2.95-3.070.27381320.19762753X-RAY DIFFRACTION100
3.07-3.210.22671320.19722765X-RAY DIFFRACTION100
3.21-3.380.25431460.18992741X-RAY DIFFRACTION100
3.38-3.590.24721500.1912756X-RAY DIFFRACTION100
3.59-3.870.25271460.17392782X-RAY DIFFRACTION99.93
3.87-4.260.19911530.15122753X-RAY DIFFRACTION100
4.26-4.870.16461310.13912831X-RAY DIFFRACTION100
4.87-6.130.2021400.16712824X-RAY DIFFRACTION100
6.14-48.290.19931430.18132963X-RAY DIFFRACTION99.81
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)
12.468619890240.8324462549860.6048598336392.530237433260.8257333341822.9019617152-0.00602523795284-0.1100141311640.03059012528650.139605112541-0.004239006174340.00297825299073-0.1383362733680.120035865660.005652217324240.2151530430460.01066743850560.01513365268440.1859226453550.02584826539290.2170729564818.508264829827.554177395434.5935842439
21.805133345510.4378875408170.9801934199330.4547758952010.4466116975912.05075135596-0.1488877602910.08686145932460.0748862292932-0.1045025749520.0762486975808-0.0106307495452-0.2049631301080.1140652234920.09373304761790.277245424156-0.01180441795310.01560809893710.1907416026710.01439349596410.25662718743111.678070136827.982958697417.4185683482
32.09449202509-0.787369350386-0.189099684622.593100102530.4944613641212.145605954160.06731606591910.33589608835-0.144565615993-0.444794083779-0.0451237955004-0.0286100114294-0.02468159724160.0298408310697-0.02244703584150.350274227433-0.0494182039925-0.01083895731010.282299068409-0.04349675836970.2580865381797.1707951605411.8898391539-3.22250364085
43.93989748701-2.6742995363-2.763920383769.021395947876.403440656758.866167222340.5059615449880.268989547619-0.300693369245-0.758399912811-1.003977312381.39003716527-0.356989719934-1.711600869010.4295424184110.5502949286760.0495637564963-0.2274594943730.744128751403-0.1574127494860.692188253676-10.420568059213.4514536083-7.12078095931
53.522616614151.51129641179-3.300574839288.43489260351-1.453113220043.13312658630.2148999265420.2287939622550.315022607186-0.1244554853350.2515872379230.162915377251-0.464997755279-0.167316049442-0.4521500482510.198555267874-0.011173419683-0.04530677589980.3536789951230.0231709246070.280888424309-23.876914931521.40851900824.1415384765
66.001394585727.61009919979-4.630015488949.65295824819-5.905553568945.09443467257-0.08483327549020.2507492354660.02649013455980.3703982894990.4526239805120.397773261152-0.0134310821233-0.479369011583-0.3508234224880.2668144783460.06847368784940.007689616006050.3280939647210.07116261105540.548688228278-36.080207753112.976656952432.7725934923
72.704700245930.484542046482-0.5481353912284.31430160913-4.397579577124.46933513749-0.244326323930.226336234322-0.211776610698-0.8693142433650.0202939638925-0.2679120569520.722841947619-0.1001059384260.2137641615710.451639539826-0.0135258026273-0.006989005481890.290256314207-0.01711068082850.371995734778-28.225613056312.271894504623.6805021581
85.50383699733-0.329417470519-2.505967729078.85606852167-1.15840581787.87334550824-0.550398937544-0.251768950003-0.877287617403-0.1792851067870.335564592514-0.829059567221.333297765920.3330467589140.2318460416320.4515903730670.00577328824970.09229268819980.28448993245-0.002807101101690.549660634491-26.3371230441.6707240206832.0137426788
94.484713861335.70283520321-3.890829910918.92624468717-4.928704335663.43860705182-0.09627442534640.7572146023440.157529747352-0.2409740079170.2875772530971.238408998580.206102160921-0.271727729463-0.1439672326080.312588027287-0.0505440744164-0.0748661425950.4783805213030.1305925542560.620683602343-37.284778436510.08118710527.3962413498
103.22867456022.31886988839-1.446740664315.04208431235-2.119629407913.43206115081-0.0898450569998-0.205256953339-0.409434457538-0.178115336741-0.0712475834416-0.04392960507820.217165897730.08047867236470.1573959921120.2542680471180.04691267145730.01814402991240.2666013146420.01682353907080.358712180122-28.67822509788.1693396326732.4375746645
113.946179830250.403708611761-0.0931975026162.25310813149-0.1511258449593.42752319648-0.0789956226539-0.110525051099-0.0218516701138-0.08385295792650.0003569904098530.136460507958-0.067385330332-0.06935097013640.0657173932150.1943830105650.01796982088380.01228768724190.160970266570.001814467810730.258772003115-12.795403407528.425225848226.711215863
123.45614704961-0.5400940667622.105716420080.463780101498-0.4414459884862.84221979097-0.258554413758-0.7399627430360.1450786347030.184244752430.1689069017190.100080858854-0.162080027675-0.524216605210.08853056289360.2949931686320.08361939582670.04299888126470.368822412226-0.02902734852990.27991920543-5.6355096518831.497892085343.5814128957
131.702888801570.4416148270430.05356453912011.79923913116-0.3572964731892.169752933640.145564976568-1.84085484875-0.1586187091460.60540234779-0.166975342598-0.02800469281970.0275305185884-0.9515227006420.02420158255130.6299125854790.1076683430330.05335308715161.331342887350.1217778306060.2576482439421.9734784695325.624495436868.3114926548
140.4758801323560.164422366002-0.7710727043180.632898397535-0.2252071712511.295196120860.107376066858-1.3273392958-0.7775003538470.5162700224110.03646107733140.1870985911820.713420524839-0.90098096557-0.0306332077340.791640195442-0.2549868510940.07282953609121.471849507730.5104813847930.666626781088-7.7494136271411.376448091864.9944865938
152.05559378760.761383611735-2.206636032113.46300263886-1.18092270144.725934361290.296711978117-0.684063333697-0.5255821992680.835497345559-0.16984126395-0.7503647727230.3037043922670.285120055432-0.2218778274190.7668098637810.0326766956123-0.1920718273811.197348439430.3401380428070.76249001465314.72184431918.562132274670.9738738297
165.7052827141-1.83126550376-4.45396147979.522347847931.358283387793.535929032870.340123016294-0.133113065475-0.0348951535014-0.05435353906450.0534980919394-0.620811413074-0.8152726272130.40958192298-0.3795470032630.264826996792-0.020347820426-0.07361972410590.403093414256-0.04443580213960.30128455929728.934404748219.408200246338.7148523903
176.03796077648-2.76434358672-1.837390142185.962626983351.119940699139.503527584181.164522153060.575500232087-0.246847525639-2.47136448334-0.52172273364-0.9732262942520.9099252333111.01261727664-0.5792636439050.7450103757590.0523635789432-0.05463416077170.671902651813-0.2902892282050.88095520848443.3985252141-0.26394096078827.1085123708
183.1516986971-0.3493465180540.9102582424426.088430064851.059181144943.403768115990.107982489401-0.0390042368735-0.5096090787440.3539750877080.183832167372-0.5822532755760.4109971046040.119038377271-0.2860921018590.253491844434-0.0336548411111-0.08330306518340.3135185108490.02383297524850.55237704276732.72147542749.5344808746937.1489098607
197.46268056232-5.49181438274-3.363583358664.053331643952.778656332387.11885145276-0.329121455162-0.455296084263-0.65704329035-0.213587463011-0.0296879647398-0.5089711095430.6964866632860.2383781539510.3574184775110.3933067438250.0167221687403-0.01662912983610.3975221467970.04519647532150.76653187332440.78367675996.0474590980637.3450608463
206.158522586791.167048046033.012476539444.633294809130.04688383859062.38296745028-0.1804155631890.0862731396421-1.288890354860.0777875402723-0.290850927035-0.07576149922810.966530994122-0.03818400625760.4141274926630.6158240363990.08829868430590.009206861122030.47521172675-0.01634360844321.3129217309437.9069428936-7.3428657251228.530806141
214.75099559298-0.8665045800550.3152076578956.28778870454-0.3213412966542.615163034910.1154162309510.272201325757-0.9829286690090.2255066038680.0647201825764-0.2524571397280.339144761840.20786238846-0.1571632749980.321452023124-0.0153241688527-0.09167883932190.257520248502-0.02807044880640.5418763799930.03158991378.1649385236534.0128324117
227.55848613302-2.113254572812.210429720076.25585482613-1.108871789259.803707374950.0923199221053-0.484575236375-0.8335116938720.152382887282-0.2200268200360.006610067616171.00343872763-0.2742248426030.03393227416580.368378136739-0.05203600531540.01766673634460.328778184591-0.0009808090729680.48360555851521.03234021096.2757946126823.2329648393
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 142 )
2X-RAY DIFFRACTION2chain 'A' and (resid 143 through 274 )
3X-RAY DIFFRACTION3chain 'A' and (resid 275 through 453 )
4X-RAY DIFFRACTION4chain 'A' and (resid 454 through 476 )
5X-RAY DIFFRACTION5chain 'A' and (resid 477 through 488 )
6X-RAY DIFFRACTION6chain 'A' and (resid 489 through 514 )
7X-RAY DIFFRACTION7chain 'A' and (resid 515 through 528 )
8X-RAY DIFFRACTION8chain 'A' and (resid 529 through 539 )
9X-RAY DIFFRACTION9chain 'A' and (resid 540 through 546 )
10X-RAY DIFFRACTION10chain 'A' and (resid 547 through 580 )
11X-RAY DIFFRACTION11chain 'B' and (resid 52 through 142 )
12X-RAY DIFFRACTION12chain 'B' and (resid 143 through 274 )
13X-RAY DIFFRACTION13chain 'B' and (resid 275 through 375 )
14X-RAY DIFFRACTION14chain 'B' and (resid 376 through 453 )
15X-RAY DIFFRACTION15chain 'B' and (resid 454 through 476 )
16X-RAY DIFFRACTION16chain 'B' and (resid 477 through 488 )
17X-RAY DIFFRACTION17chain 'B' and (resid 489 through 501 )
18X-RAY DIFFRACTION18chain 'B' and (resid 502 through 539 )
19X-RAY DIFFRACTION19chain 'B' and (resid 540 through 546 )
20X-RAY DIFFRACTION20chain 'B' and (resid 547 through 554 )
21X-RAY DIFFRACTION21chain 'B' and (resid 555 through 580 )
22X-RAY DIFFRACTION22chain 'C' and (resid 1 through 12 )

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