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- PDB-4n3c: Crystal Structure of human O-GlcNAc Transferase bound to a peptid... -

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Basic information

Entry
Database: PDB / ID: 4n3c
TitleCrystal Structure of human O-GlcNAc Transferase bound to a peptide from HCF-1 pro-repeat2(1-26) and UDP-GlcNAc
Components
  • Host cell factor 1
  • UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
KeywordsTRANSFERASE/SUBSTRATE / Glycosyltransferase / O-GlcNAc Transferase / Proteolysis Substrate / TPR domain / TPR binding / TRANSFERASE-SUBSTRATE complex
Function / homology
Function and homology information


protein N-acetylglucosaminyltransferase complex / protein O-GlcNAc transferase / release from viral latency / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of necroptotic process / regulation of Rac protein signal transduction / negative regulation of stem cell population maintenance ...protein N-acetylglucosaminyltransferase complex / protein O-GlcNAc transferase / release from viral latency / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of necroptotic process / regulation of Rac protein signal transduction / negative regulation of stem cell population maintenance / protein O-linked glycosylation / Set1C/COMPASS complex / MLL1/2 complex / NSL complex / regulation of glycolytic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / RIPK1-mediated regulated necrosis / regulation of synapse assembly / histone methyltransferase complex / regulation of gluconeogenesis / positive regulation of stem cell population maintenance / Formation of WDR5-containing histone-modifying complexes / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of proteolysis / mitophagy / hemopoiesis / MLL1 complex / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / histone acetyltransferase complex / regulation of protein-containing complex assembly / positive regulation of cell cycle / positive regulation of lipid biosynthetic process / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / negative regulation of cell migration / response to nutrient / cell projection / positive regulation of translation / mitochondrial membrane / cellular response to glucose stimulus / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / response to insulin / Transcriptional activation of mitochondrial biogenesis / Regulation of necroptotic cell death / protein processing / chromatin DNA binding / UCH proteinases / chromatin organization / protein-macromolecule adaptor activity / positive regulation of cold-induced thermogenesis / HATs acetylate histones / DNA-binding transcription factor binding / transcription coactivator activity / protein stabilization / chromatin remodeling / cadherin binding / cell cycle / neuronal cell body / glutamatergic synapse / apoptotic process / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Host cell factor / Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / Kelch motif / Galactose oxidase, central domain / Rossmann fold - #11380 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / TPR repeat / Tetratricopeptide repeat ...Host cell factor / Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / Kelch motif / Galactose oxidase, central domain / Rossmann fold - #11380 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / TPR repeat / Tetratricopeptide repeat / Kelch repeat type 1 / Kelch motif / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Kelch-type beta propeller / Tetratricopeptide repeat domain / Tetratricopeptide repeat / Glycogen Phosphorylase B; / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Immunoglobulin-like fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / Host cell factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsLazarus, M.B. / Herr, W. / Walker, S.
CitationJournal: Science / Year: 2013
Title: HCF-1 is cleaved in the active site of O-GlcNAc transferase.
Authors: Lazarus, M.B. / Jiang, J. / Kapuria, V. / Bhuiyan, T. / Janetzko, J. / Zandberg, W.F. / Vocadlo, D.J. / Herr, W. / Walker, S.
History
DepositionOct 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: Host cell factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2773
Polymers83,6692
Non-polymers6071
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-12 kcal/mol
Surface area27380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.880, 98.880, 365.930
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / O-GlcNAc transferase subunit p110 / O-linked N-acetylglucosamine transferase 110 kDa subunit / OGT


Mass: 80974.508 Da / Num. of mol.: 1 / Fragment: UNP residues 323-1041
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGT / Plasmid: pET23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15294, protein O-GlcNAc transferase
#2: Protein/peptide Host cell factor 1


Mass: 2694.862 Da / Num. of mol.: 1 / Fragment: UNP residues 1072-1097 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P51610
#3: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.09 Å3/Da / Density % sol: 60.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.86M Potassium Phosphate Dibasic, 0.86M Sodium Phosphate Monobasic, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.55→85.633 Å / Num. all: 33955 / Num. obs: 33955 / % possible obs: 96.1 % / Redundancy: 3 % / Biso Wilson estimate: 39 Å2 / Rsym value: 0.151 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.55-2.693.10.8070.81437546550.80792.7
2.69-2.853.10.5321.21391345460.53294.9
2.85-3.052.90.3321.91289843830.33297.4
3.05-3.2930.22331232540950.22396.6
3.29-3.613.10.1524.51158337970.15298.2
3.61-4.0330.1225.41020134540.12297.4
4.03-4.6630.0976.6915830770.09796.9
4.66-5.730.0818776426260.08196.4
5.7-8.062.90.0728.9598520970.07297.2
8.06-70.0862.70.0646.5333312250.06494.4

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→62.517 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8554 / SU ML: 0.28 / σ(F): 1.36 / Phase error: 21.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 1692 4.99 %
Rwork0.1837 --
obs0.1858 33941 95.01 %
all-35633 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.52 Å2 / Biso mean: 50.0115 Å2 / Biso min: 27.92 Å2
Refinement stepCycle: LAST / Resolution: 2.55→62.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5648 0 39 102 5789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035836
X-RAY DIFFRACTIONf_angle_d0.7497931
X-RAY DIFFRACTIONf_chiral_restr0.051885
X-RAY DIFFRACTIONf_plane_restr0.0031028
X-RAY DIFFRACTIONf_dihedral_angle_d13.372184
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.62510.30841250.24532486261191
2.6251-2.70980.24321480.24032554270293
2.7098-2.80670.2941430.2322560270393
2.8067-2.91910.28821260.22662710283697
2.9191-3.05190.24971370.22232658279596
3.0519-3.21280.25251360.20542734287097
3.2128-3.41410.24491340.18392645277995
3.4141-3.67770.22061530.17062727288097
3.6777-4.04770.20271360.14992718285496
4.0477-4.63320.17771460.14382744289096
4.6332-5.83670.19861510.16132774292595
5.8367-62.5360.22361570.19312939309694
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)
16.52080.0535-1.10318.1987.65039.2375-0.7366-0.9288-0.47910.6935-0.10040.31070.4852-0.93480.61360.45710.14160.07350.6282-0.06690.4458-19.1924-42.084761.2719
27.1733-3.23992.57316.6325-6.68437.78640.1332-0.08360.28680.22390.0496-0.0621-1.0093-0.1691-0.20520.47780.08450.07690.486-0.13280.4306-13.4188-36.565155.3715
32.26720.2560.12873.68960.35932.3166-0.0373-0.1743-0.02630.18990.107-0.01830.0142-0.0821-0.05150.30570.025-0.00250.4081-0.00410.2967-6.0984-49.72149.354
40.1118-0.06210.60012.3435-2.08036.3527-0.0578-0.0573-0.0301-0.00470.15050.28060.1558-0.7102-0.07250.2145-0.02490.0240.46080.01220.3159-17.3166-53.136530.2505
56.81522.88813.12668.95-0.37774.76380.2421-0.13830.18470.1648-0.15280.09-0.5588-0.3587-0.12220.31350.06650.0320.4636-0.00480.3124-19.6033-35.598928.7751
61.3541-0.204-0.43671.29590.54773.47510.0789-0.09630.35070.0690.0511-0.2538-0.72460.2986-0.13440.443-0.11190.00960.331-0.02220.42695.2002-27.811926.195
79.8896-2.8394-1.77982.0679-2.4728.3925-0.04851.1093-0.3146-0.62750.02720.58620.0052-0.536-0.12080.48780.0333-0.01830.59060.05260.44144.7526-47.7707-12.5583
85.7025-0.0513-1.4165.6845-2.88299.18810.20570.74620.1284-0.6651-0.2986-0.2753-0.11120.3410.02640.3496-0.01050.09330.5596-0.02260.349613.644-50.1381-11.3186
94.22560.1384-1.15351.28080.49091.76870.0341-0.06360.0237-0.0683-0.1055-0.107-0.06940.32950.07240.2543-0.03470.04460.35180.02460.347813.0441-52.16571.6263
104.41070.48220.29832.9263-1.28564.37390.09270.4212-0.1153-0.32160.12020.22480.1289-0.5448-0.1620.22-0.0074-0.03140.3680.00410.2965-12.4363-48.39893.8465
116.7059-1.2942-1.98422.17160.60033.5616-0.08580.513-0.7359-0.23580.08180.48290.2637-1.32080.07830.3593-0.1026-0.07090.6880.07130.4479-15.6966-54.9593.6876
121.1341-0.8366-0.2251.9752-0.07423.10120.16690.08290.1038-0.1714-0.00050.1077-0.457-0.2244-0.14050.30350.00170.00950.39960.05970.3582-4.372-37.01885.1622
134.0201-1.2431-2.59832.85032.34578.8773-0.02980.28050.1487-0.2513-0.07060.3302-0.7962-0.92790.05610.40750.11-0.08010.60930.09190.3958-16.3212-36.1864-4.4806
146.19351.69141.64824.77172.03885.02760.0081.01840.6369-0.6066-0.1806-0.3572-0.87510.35560.19470.440.01990.05760.52930.15350.41940.5101-32.9825-6.7213
151.62590.122-0.43284.95253.22154.71040.0890.11740.6273-0.34890.07170.1349-1.68080.2476-0.22790.8905-0.08640.04340.33540.09830.66543.8501-16.294718.5019
162.4137-2.4397-1.51116.5164-0.76842.2843-0.0643-0.715-0.57510.4592-0.27920.43080.63840.14890.2560.6604-0.001-0.05080.64760.07650.7577-0.9384-45.50821.7729
178.6621-2.4947-5.4396.35062.37553.52090.4937-0.49660.28910.63350.12670.3391-0.0623-0.3734-0.67930.3456-0.0865-0.00340.47640.04330.386-15.8795-47.493446.0381
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 313:325)A313 - 325
2X-RAY DIFFRACTION2(CHAIN A AND RESID 326:346)A326 - 346
3X-RAY DIFFRACTION3(CHAIN A AND RESID 347:408)A347 - 408
4X-RAY DIFFRACTION4(CHAIN A AND RESID 409:476)A409 - 476
5X-RAY DIFFRACTION5(CHAIN A AND RESID 477:515)A477 - 515
6X-RAY DIFFRACTION6(CHAIN A AND RESID 516:706)A516 - 706
7X-RAY DIFFRACTION7(CHAIN A AND RESID 707:723)A707 - 723
8X-RAY DIFFRACTION8(CHAIN A AND RESID 724:786)A724 - 786
9X-RAY DIFFRACTION9(CHAIN A AND RESID 787:828)A787 - 828
10X-RAY DIFFRACTION10(CHAIN A AND RESID 829:876)A829 - 876
11X-RAY DIFFRACTION11(CHAIN A AND RESID 877:895)A877 - 895
12X-RAY DIFFRACTION12(CHAIN A AND RESID 896:959)A896 - 959
13X-RAY DIFFRACTION13(CHAIN A AND RESID 960:977)A960 - 977
14X-RAY DIFFRACTION14(CHAIN A AND RESID 978:995)A978 - 995
15X-RAY DIFFRACTION15(CHAIN A AND RESID 996:1028)A996 - 1028
16X-RAY DIFFRACTION16(CHAIN B AND RESID 5:13)B5 - 13
17X-RAY DIFFRACTION17(CHAIN B AND RESID 14:24)B14 - 24

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