[English] 日本語
Yorodumi
- PDB-4n3a: Crystal Structure of human O-GlcNAc transferase bound to a peptid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4n3a
TitleCrystal Structure of human O-GlcNAc transferase bound to a peptide from HCF-1 pro-repeat 2 (1-26)E10A
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 neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of glycolytic process / 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 / positive regulation of proteolysis / phosphatidylinositol-3,4,5-trisphosphate binding / MLL1 complex / mitophagy / hemopoiesis / 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 / response to nutrient / negative regulation of cell migration / positive regulation of translation / cell projection / cellular response to glucose stimulus / mitochondrial membrane / 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 / protein-macromolecule adaptor activity / positive regulation of cold-induced thermogenesis / chromatin organization / 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 / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
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-5'-DIPHOSPHATE / 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: 1.88 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)84,0153
Polymers83,6112
Non-polymers4041
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-9 kcal/mol
Surface area27890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.929, 98.929, 367.015
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
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: 2636.826 Da / Num. of mol.: 1 / Fragment: HCF-1 pro-repeat2 (UNP residues 1072-1097) / Mutation: E10A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P51610
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THIS IS A MUTATION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.72M Potassium Phosphate Monobasic, 0.88M Potassium Phosphate Dibasic, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.88→85.675 Å / Num. all: 82602 / Num. obs: 82602 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rsym value: 0.087 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.88-1.983.80.5991.146145120250.59996.1
1.98-2.13.60.3451.940743112740.34595
2.1-2.253.40.2382.435476105730.23894.7
2.25-2.433.20.1882.43143198750.18895.2
2.43-2.663.20.1353.82875689300.13593.4
2.66-2.973.40.1055.82667779250.10591.1
2.97-3.433.40.096.92544674300.0995.5
3.43-4.24.10.0847.42677165170.08498.2
4.2-5.9560.06993081751710.06998.4
5.95-45.8587.90.05312.22285328820.05393.6

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→45.858 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.852 / SU ML: 0.24 / σ(F): 1.35 / Phase error: 21.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 4135 5.01 %Random
Rwork0.2004 ---
obs0.2015 82481 94.31 %-
all-86616 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.6 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 106.9 Å2 / Biso mean: 39.2433 Å2 / Biso min: 15.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.1762 Å2-0 Å2-0 Å2
2--0.1762 Å20 Å2
3----0.3524 Å2
Refinement stepCycle: LAST / Resolution: 1.88→45.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5588 0 25 148 5761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075767
X-RAY DIFFRACTIONf_angle_d1.0627835
X-RAY DIFFRACTIONf_chiral_restr0.071872
X-RAY DIFFRACTIONf_plane_restr0.0051016
X-RAY DIFFRACTIONf_dihedral_angle_d132158
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.88-1.90140.3991410.33512602274395
1.9014-1.92370.32021240.32062605272997
1.9237-1.94720.33191320.28282593272595
1.9472-1.97180.28391570.2642591274897
1.9718-1.99780.26431600.25192568272896
1.9978-2.02520.30271080.2522623273195
2.0252-2.05410.28451340.24542562269695
2.0541-2.08470.26021460.25352572271895
2.0847-2.11730.29421330.23942578271194
2.1173-2.1520.24541490.23332543269293
2.152-2.18910.24881360.21782539267593
2.1891-2.2290.25471290.22232586271595
2.229-2.27180.24471170.21852607272495
2.2718-2.31820.26091340.21522599273394
2.3182-2.36860.24681420.22462589273195
2.3686-2.42370.28181410.21992570271194
2.4237-2.48430.24161550.2242551270693
2.4843-2.55150.26211200.2232540266092
2.5515-2.62650.25591220.21692508263091
2.6265-2.71130.22111280.20582511263991
2.7113-2.80820.23241380.20852486262490
2.8082-2.92060.23031160.2112508262490
2.9206-3.05350.23311510.20342533268492
3.0535-3.21450.20111340.20652639277394
3.2145-3.41580.21081290.19082734286397
3.4158-3.67940.23131480.18272745289398
3.6794-4.04950.19111520.16422746289897
4.0495-4.6350.1681480.15032793294197
4.635-5.83770.17121750.16572819299498
5.8377-45.87170.19981360.19972906304292
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)
13.9705-0.40080.20762.15850.59863.6710.0465-0.16970.2714-0.03020.05630.0644-0.4179-0.3287-0.07440.31150.14990.0690.4395-0.09270.3309-16.2921-38.319856.6552
21.74130.028-0.25591.1335-0.20551.3386-0.1062-0.41970.20640.18860.13180.0043-0.1-0.0438-0.03790.23020.06150.02380.3796-0.04840.2381-6.9874-46.483155.3624
31.50020.10850.48131.42290.07192.56640.05170.1129-0.03510.05350.0873-0.06880.1243-0.2913-0.08230.1852-0.0129-0.01570.23370.01430.1634-8.9163-55.233641.9158
40.2129-0.0398-0.27741.3001-0.24172.39690.0011-0.170.079-0.0140.06450.04030.0938-0.3853-0.04730.16830.01790.00310.4440.04470.2448-18.4982-51.488826.6612
52.21680.62560.18852.39450.12771.67340.1201-0.45440.2640.2336-0.02180.143-0.2492-0.1959-0.03180.27520.10330.05280.4745-0.01050.3164-19.3577-35.75428.8413
60.845-0.37550.01260.85360.48031.94680.0333-0.25420.30160.23680.0723-0.1843-0.33140.3959-0.05540.3581-0.1132-0.02950.4143-0.12120.42358.7467-28.419429.7861
70.6651-0.073-0.33661.22180.12441.70230.08670.02710.37750.07730.04030.0613-0.4727-0.1249-0.06840.26050.01640.02240.2531-0.01120.3972-2.5743-26.208616.5351
82.111-0.5963-1.64222.1567-0.42891.83070.03960.36660.2188-0.5815-0.3628-0.12550.05840.51860.20830.24-0.02120.06630.6320.11740.260111.6869-46.6597-11.6838
92.85130.3115-0.47060.875-0.89213.72520.14360.7321-0.0365-0.4394-0.17880.15430.1465-0.12870.11770.3224-0.03290.08050.493-0.05460.299511.167-52.1631-12.4416
101.5619-0.1154-0.5540.5261-0.08321.1196-0.10630.1122-0.0683-0.06750.0429-0.0840.0160.06550.02560.1565-0.03850.0030.29470.01030.21944.8376-50.27092.6784
111.601-0.4335-0.03331.2301-0.91461.0419-0.06560.3326-0.1159-0.170.14190.16450.1957-0.3004-0.03540.1588-0.0462-0.03980.35590.04520.2121-13.2896-50.04213.1816
121.3704-0.2854-0.28140.6634-0.05831.8333-0.00460.24940.2282-0.09270.07470.0267-0.1614-0.2681-0.03740.1484-0.0056-0.00480.2910.07740.24-6.0808-38.19331.9926
131.4837-0.49690.37911.50490.9681.0077-0.09970.56561.013-0.0022-0.24120.0171-1.4990.21410.17120.9004-0.1505-0.01330.1887-0.05610.78212.5791-13.147321.7367
141.7955-0.3207-1.64783.0205-0.16269.4910.0699-0.08560.20420.25550.0478-0.02980.05920.04310.00990.24640.05080.05360.46720.11170.3074-14.3927-47.210844.5632
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 313:341)A313 - 341
2X-RAY DIFFRACTION2(CHAIN A AND RESID 342:382)A342 - 382
3X-RAY DIFFRACTION3(CHAIN A AND RESID 383:429)A383 - 429
4X-RAY DIFFRACTION4(CHAIN A AND RESID 430:474)A430 - 474
5X-RAY DIFFRACTION5(CHAIN A AND RESID 475:518)A475 - 518
6X-RAY DIFFRACTION6(CHAIN A AND RESID 519:654)A519 - 654
7X-RAY DIFFRACTION7(CHAIN A AND RESID 655:706)A655 - 706
8X-RAY DIFFRACTION8(CHAIN A AND RESID 707:742)A707 - 742
9X-RAY DIFFRACTION9(CHAIN A AND RESID 743:784)A743 - 784
10X-RAY DIFFRACTION10(CHAIN A AND RESID 785:849)A785 - 849
11X-RAY DIFFRACTION11(CHAIN A AND RESID 850:876)A850 - 876
12X-RAY DIFFRACTION12(CHAIN A AND RESID 877:1003)A877 - 1003
13X-RAY DIFFRACTION13(CHAIN A AND RESID 1004:1028)A1004 - 1028
14X-RAY DIFFRACTION14(CHAIN B AND RESID 13:24)B13 - 24

+
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