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- PDB-4ee3: Crystal structure of human M340H-beta-1,4-galactosyltransferase-1... -

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Basic information

Entry
Database: PDB / ID: 4ee3
TitleCrystal structure of human M340H-beta-1,4-galactosyltransferase-1 (M340H-B4GAL-T1) in complex with pentasaccharide
ComponentsBeta-1,4-galactosyltransferase 1
KeywordsTRANSFERASE / Protein-carbohydrate complex / GT-A fold / glycosyltransferase
Function / homology
Function and homology information


Defective B4GALT1 causes CDG-2d / galactosyltransferase activity / Interaction With Cumulus Cells And The Zona Pellucida / Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) / Lactose synthesis / Keratan sulfate biosynthesis / lactose synthase / neolactotriaosylceramide beta-1,4-galactosyltransferase / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase / N-acetyllactosamine synthase ...Defective B4GALT1 causes CDG-2d / galactosyltransferase activity / Interaction With Cumulus Cells And The Zona Pellucida / Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) / Lactose synthesis / Keratan sulfate biosynthesis / lactose synthase / neolactotriaosylceramide beta-1,4-galactosyltransferase / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase / N-acetyllactosamine synthase / N-acetyllactosamine synthase activity / positive regulation of circulating fibrinogen levels / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity / Golgi trans cisterna / N-Glycan antennae elongation / penetration of zona pellucida / UDP-galactosyltransferase activity / regulation of acrosome reaction / lactose synthase activity / lactose biosynthetic process / oligosaccharide biosynthetic process / macrophage migration / development of secondary sexual characteristics / desmosome / acute inflammatory response / galactose metabolic process / Pre-NOTCH Processing in Golgi / positive regulation of epithelial cell proliferation involved in wound healing / binding of sperm to zona pellucida / protein N-linked glycosylation / angiogenesis involved in wound healing / Transferases; Glycosyltransferases; Hexosyltransferases / azurophil granule membrane / Golgi cisterna membrane / epithelial cell development / alpha-tubulin binding / beta-tubulin binding / extracellular matrix organization / secretory granule membrane / epithelial cell proliferation / filopodium / brush border membrane / lipid metabolic process / negative regulation of epithelial cell proliferation / manganese ion binding / basolateral plasma membrane / cell adhesion / positive regulation of apoptotic process / Golgi membrane / external side of plasma membrane / Neutrophil degranulation / Golgi apparatus / protein-containing complex / extracellular space / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
Beta-1,4-galactosyltransferase / Galactosyltransferase, N-terminal / N-terminal region of glycosyl transferase group 7 / Galactosyltransferase, C-terminal / N-terminal domain of galactosyltransferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / 6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE / Beta-1,4-galactosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Molecular placement / Resolution: 2.3 Å
AuthorsRamakrishnan, B. / Qasba, P.K.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Binding of N-acetylglucosamine (GlcNAc) beta 1-6-branched oligosaccharide acceptors to beta 4-galactosyltransferase I reveals a new ligand binding mode.
Authors: Ramakrishnan, B. / Boeggeman, E. / Qasba, P.K.
History
DepositionMar 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Apr 2, 2014Group: Other
Revision 1.3Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: 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
Revision 2.2Oct 9, 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

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Assembly

Deposited unit
A: Beta-1,4-galactosyltransferase 1
B: Beta-1,4-galactosyltransferase 1
C: Beta-1,4-galactosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,73233
Polymers98,3203
Non-polymers6,41330
Water9,494527
1
A: Beta-1,4-galactosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,10313
Polymers32,7731
Non-polymers2,33012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-1,4-galactosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,91111
Polymers32,7731
Non-polymers2,13810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-1,4-galactosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7199
Polymers32,7731
Non-polymers1,9458
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Beta-1,4-galactosyltransferase 1
B: Beta-1,4-galactosyltransferase 1
C: Beta-1,4-galactosyltransferase 1
hetero molecules

A: Beta-1,4-galactosyltransferase 1
B: Beta-1,4-galactosyltransferase 1
C: Beta-1,4-galactosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,46566
Polymers196,6396
Non-polymers12,82560
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area33380 Å2
ΔGint-595 kcal/mol
Surface area65500 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15340 Å2
ΔGint-284 kcal/mol
Surface area34100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.612, 195.158, 143.695
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Sugars , 2 types, 6 molecules ABC

#1: Protein Beta-1,4-galactosyltransferase 1 / Beta-1 / 4-GalTase 1 / Beta4Gal-T1 / b4Gal-T1 / UDP-Gal:beta-GlcNAc beta-1 / 4- ...Beta-1 / 4-GalTase 1 / Beta4Gal-T1 / b4Gal-T1 / UDP-Gal:beta-GlcNAc beta-1 / 4-galactosyltransferase 1 / UDP-galactose:beta-N-acetylglucosamine beta-1 / 4-galactosyltransferase 1 / Lactose synthase A protein / N-acetyllactosamine synthase / Nal synthase / Beta-N-acetylglucosaminylglycopeptide beta-1 / 4-galactosyltransferase / Beta-N-acetylglucosaminyl-glycolipid beta-1 / 4-galactosyltransferase / Processed beta-1 / 4-galactosyltransferase 1


Mass: 32773.230 Da / Num. of mol.: 3 / Fragment: Catalytic domain / Mutation: R337T, C338T, M340H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B4GALT1, beta4Gal-T1, GGTB2 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P15291, Transferases; Glycosyltransferases; Hexosyltransferases, lactose synthase, N-acetyllactosamine synthase, beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase
#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[2-acetamido-2-deoxy- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGlcpNAcb1-3[DGlcpNAcb1-6]DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5][a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-3-2-3/a4-b1_b3-c1_b6-e1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}}[(6+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 554 molecules

#3: Chemical ChemComp-UDH / 6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE


Mass: 503.335 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H27N3O12P2
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsIN THE ELECTRON DENSITY MAPS OF ALL THREE MOLECULES THE ELECTRON DENSITY FOR THE GLYCOSIDIC BOND ...IN THE ELECTRON DENSITY MAPS OF ALL THREE MOLECULES THE ELECTRON DENSITY FOR THE GLYCOSIDIC BOND BETWEEN RESIDUES NAG(404) AND GAL(405) IS CLEARLY OBSERVED. HOWEVER, IT EXTENDS ONLY TO THE CYCLIC ATOMS OF THE GAL(405) MOIETY.

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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: 3.84 Å3/Da / Density % sol: 67.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Mes buffer, 1.6 M ammonium sulfate, 2% Dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 9, 2005 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 57756 / % possible obs: 91 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Rsym value: 0.092 / Net I/σ(I): 17.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 4424 / Rsym value: 0.366 / % possible all: 66.7

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Processing

Software
NameClassification
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: Molecular placement
Starting model: PDB entry 2AEC

2aec


Resolution: 2.3→36.31 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.449 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.237 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24014 3056 5 %RANDOM
Rwork0.18658 ---
obs0.18922 55796 90.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.054 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→36.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6654 0 392 527 7573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227229
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9482.0099862
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3485816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44323.59351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49414.5261152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4881551
X-RAY DIFFRACTIONr_chiral_restr0.1560.21070
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215430
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.1291.54101
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1126672
X-RAY DIFFRACTIONr_scbond_it3.58733128
X-RAY DIFFRACTIONr_scangle_it5.5134.53190
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 158 -
Rwork0.258 2979 -
obs--64.15 %

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