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- PDB-6apl: Crystal Structure of human ST6GALNAC2 in complex with CMP -

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Basic information

Entry
Database: PDB / ID: 6apl
TitleCrystal Structure of human ST6GALNAC2 in complex with CMP
ComponentsAlpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
KeywordsTRANSFERASE / glycosyltransferase / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase / alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity / protein sialylation / Maturation of protein 3a / sialyltransferase activity / Maturation of protein 3a / Termination of O-glycan biosynthesis / O-glycan processing / Sialic acid metabolism / protein O-linked glycosylation ...alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase / alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity / protein sialylation / Maturation of protein 3a / sialyltransferase activity / Maturation of protein 3a / Termination of O-glycan biosynthesis / O-glycan processing / Sialic acid metabolism / protein O-linked glycosylation / protein glycosylation / transferase activity / Maturation of spike protein / viral protein processing / Golgi membrane
Similarity search - Function
Glycosyl transferase family 29 / Sialyltransferase / GT29-like superfamiliy / Glycosyltransferase family 29 (sialyltransferase)
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsForouhar, F. / Moremen, K.W. / Northeast Structural Genomics Consortium (NESG) / Tong, L.
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Expression system for structural and functional studies of human glycosylation enzymes.
Authors: Moremen, K.W. / Ramiah, A. / Stuart, M. / Steel, J. / Meng, L. / Forouhar, F. / Moniz, H.A. / Gahlay, G. / Gao, Z. / Chapla, D. / Wang, S. / Yang, J.Y. / Prabhakar, P.K. / Johnson, R. / ...Authors: Moremen, K.W. / Ramiah, A. / Stuart, M. / Steel, J. / Meng, L. / Forouhar, F. / Moniz, H.A. / Gahlay, G. / Gao, Z. / Chapla, D. / Wang, S. / Yang, J.Y. / Prabhakar, P.K. / Johnson, R. / Rosa, M.D. / Geisler, C. / Nairn, A.V. / Seetharaman, J. / Wu, S.C. / Tong, L. / Gilbert, H.J. / LaBaer, J. / Jarvis, D.L.
History
DepositionAug 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jul 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_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.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
B: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
C: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
D: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
E: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
F: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,78022
Polymers253,6296
Non-polymers4,15116
Water3,873215
1
A: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0374
Polymers42,2711
Non-polymers7663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0374
Polymers42,2711
Non-polymers7663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0374
Polymers42,2711
Non-polymers7663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2585
Polymers42,2711
Non-polymers9874
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5952
Polymers42,2711
Non-polymers3231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8163
Polymers42,2711
Non-polymers5442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.168, 71.125, 138.608
Angle α, β, γ (deg.)103.69, 97.26, 103.03
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2 / / GalNAc alpha-2 / 6-sialyltransferase II / ST6GalNAc II / ST6GalNAcII / SThM / Sialyltransferase 7B / SIAT7-B


Mass: 42271.477 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ST6GALNAC2, SIAT7B, SIATL1, STHM / Plasmid: pGEn2
Details (production host): mammalian expression vector (CMV promoter)
Cell line (production host): HEK293S GNT1- / Production host: Homo sapiens (human) / References: UniProt: Q9UJ37, EC: 2.4.99.-
#2: Chemical
ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H14N3O8P
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.5 Å3/Da / Density meas: 51 Mg/m3 / Density % sol: 52.47 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 4.2
Details: 0.1M Sodium Citrate (pH 4.2), 0.1M Ammonium Sulfate, and 24% (w/v) PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18076 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 14, 2015 / Details: mirrors
RadiationMonochromator: SI III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18076 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 120969 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.042 / Χ2: 1.374 / Net I/σ(I): 19.8
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6277 / Rpim(I) all: 0.421 / Χ2: 0.659 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: the structure of apo enzyme, the associated PDB entry

Resolution: 2.35→41.605 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 27.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 10322 10.03 %
Rwork0.1961 --
obs0.2001 102956 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→41.605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14169 0 266 215 14650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414872
X-RAY DIFFRACTIONf_angle_d0.72920206
X-RAY DIFFRACTIONf_dihedral_angle_d21.1988567
X-RAY DIFFRACTIONf_chiral_restr0.0442194
X-RAY DIFFRACTIONf_plane_restr0.0052530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.37670.37143570.3013064X-RAY DIFFRACTION97
2.3767-2.40470.30373140.28323003X-RAY DIFFRACTION97
2.4047-2.4340.3293510.2733060X-RAY DIFFRACTION97
2.434-2.46480.30293590.26513056X-RAY DIFFRACTION97
2.4648-2.49720.31893530.25842999X-RAY DIFFRACTION97
2.4972-2.53140.3023220.26443140X-RAY DIFFRACTION97
2.5314-2.56760.32173350.26793039X-RAY DIFFRACTION97
2.5676-2.60590.31113230.26883082X-RAY DIFFRACTION97
2.6059-2.64660.29923350.2493098X-RAY DIFFRACTION98
2.6466-2.690.33473390.25653074X-RAY DIFFRACTION97
2.69-2.73640.29033390.2523091X-RAY DIFFRACTION97
2.7364-2.78610.29833690.24443012X-RAY DIFFRACTION98
2.7861-2.83970.28713610.2333084X-RAY DIFFRACTION98
2.8397-2.89760.29213220.23263048X-RAY DIFFRACTION98
2.8976-2.96060.26983460.23643171X-RAY DIFFRACTION98
2.9606-3.02950.2833550.24333025X-RAY DIFFRACTION98
3.0295-3.10520.3093480.25333108X-RAY DIFFRACTION98
3.1052-3.18920.27673130.25193087X-RAY DIFFRACTION98
3.1892-3.2830.27753430.2323147X-RAY DIFFRACTION98
3.283-3.38890.27833680.2343113X-RAY DIFFRACTION98
3.3889-3.50990.26993190.22023087X-RAY DIFFRACTION98
3.5099-3.65040.25593650.21563063X-RAY DIFFRACTION99
3.6504-3.81640.23563630.19573115X-RAY DIFFRACTION99
3.8164-4.01750.23230.17573167X-RAY DIFFRACTION99
4.0175-4.2690.21683410.16743103X-RAY DIFFRACTION99
4.269-4.59820.17793750.15163071X-RAY DIFFRACTION99
4.5982-5.06020.19023200.14633183X-RAY DIFFRACTION99
5.0602-5.79070.21423610.16743126X-RAY DIFFRACTION99
5.7907-7.28930.2143630.17853124X-RAY DIFFRACTION100
7.2893-41.61140.1773400.15453094X-RAY DIFFRACTION98
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)
12.0115-1.20590.19963.304-0.62321.88730.1338-0.08430.009-0.4403-0.087-0.0017-0.0740.0982-0.01630.4871-0.07530.04940.3840.01120.31280.2586-0.8814-0.5366
23.7244-0.78610.70391.64050.07262.00490.0258-0.4919-0.0431-0.06350.0505-0.0636-0.1290.0541-0.00160.4237-0.08340.04210.46760.00260.35011.5715-2.059565.7626
32.29920.50730.37332.7964-0.07662.1999-0.07650.1881-0.1064-0.07860.11090.576-0.2311-0.4544-0.09070.5020.08770.0370.5282-0.00050.4602-28.247834.6311-17.9073
42.88050.75330.34543.1669-0.04012.12010.1595-0.0586-0.67660.3439-0.0644-0.00720.4160.1676-0.01360.53460.06410.0270.53840.0560.5646-28.7889-21.546683.2459
52.0968-2.1027-0.40256.78450.62052.00050.33490.2450.1611-1.5281-0.2370.1936-0.10040.0517-0.08090.7990.0375-0.00630.37570.0350.3566-13.969926.023141.0569
67.7112-0.2334-0.84351.19820.14812.3260.0873-1.4758-0.10330.15870.0074-0.2217-0.06480.1214-0.01280.4271-0.04780.00370.79680.05380.43731.0566-9.677323.7649
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 66:374 OR RESID 402:403 ) )A66 - 374
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 66:374 OR RESID 402:403 ) )A402 - 403
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 66:374 OR RESID 402:403 ) )B66 - 374
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 66:374 OR RESID 402:403 ) )B402 - 403
5X-RAY DIFFRACTION3( CHAIN C AND ( RESID 66:374 OR RESID 402:403 ) )C66 - 374
6X-RAY DIFFRACTION3( CHAIN C AND ( RESID 66:374 OR RESID 402:403 ) )C402 - 403
7X-RAY DIFFRACTION4( CHAIN D AND ( RESID 66:374 OR RESID 402:404 ) )D66 - 374
8X-RAY DIFFRACTION4( CHAIN D AND ( RESID 66:374 OR RESID 402:404 ) )D402 - 404
9X-RAY DIFFRACTION5( CHAIN E AND RESID 66:374 )E66 - 374
10X-RAY DIFFRACTION6( CHAIN F AND ( RESID 70:374 OR RESID 402:402 ) )F70 - 374
11X-RAY DIFFRACTION6( CHAIN F AND ( RESID 70:374 OR RESID 402:402 ) )F402

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