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- PDB-4l41: Human Lactose synthase: A 2:1 complex between human alpha-lactalb... -

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Basic information

Entry
Database: PDB / ID: 4l41
TitleHuman Lactose synthase: A 2:1 complex between human alpha-lactalbumin and human beta1,4-galactosyltransferase
Components
  • Alpha-lactalbumin
  • Beta-1,4-galactosyltransferase 1
KeywordsCalcium Binding Protein/Transferase / GT-A fold / lactose synthase / Substrate binding / Golgi / Calcium Binding Protein-Transferase complex
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 / Golgi lumen / negative regulation of epithelial cell proliferation / lysozyme activity / cell-cell signaling / manganese ion binding / defense response to Gram-negative bacterium / basolateral plasma membrane / cell adhesion / defense response to Gram-positive bacterium / defense response to bacterium / positive regulation of apoptotic process / Golgi membrane / external side of plasma membrane / apoptotic process / calcium ion binding / Neutrophil degranulation / Golgi apparatus / signal transduction / protein-containing complex / extracellular space / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
Lactalbumin / 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 / Lysozyme - #10 ...Lactalbumin / 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 / Lysozyme - #10 / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Alpha-lactalbumin / Beta-1,4-galactosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRamakrishnan, B. / Qasba, P.K.
CitationJournal: To be Published
Title: Crystal Structure of Human Lactose Synthase forms a Novel 1:2 Complex between beta1,4Galactosyltransferase 1 and alpha-Lactalbumin Proteins
Authors: Ramakrishnan, B. / Qasba, P.K.
History
DepositionJun 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_conn.pdbx_dist_value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,2716
Polymers61,0953
Non-polymers1763
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-49 kcal/mol
Surface area23280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.390, 65.210, 71.720
Angle α, β, γ (deg.)90.00, 114.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-lactalbumin / Lactose synthase B protein / Lysozyme-like protein 7


Mass: 14164.206 Da / Num. of mol.: 2 / Fragment: UNP residues 19-142
Source method: isolated from a genetically manipulated source
Details: expressed with 11 amino acide N-terminal T7-tag / Source: (gene. exp.) Homo sapiens (human) / Gene: 4-galactosyltransferase, beta1, LALBA, LYZL7 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P00709
#2: Protein Beta-1,4-galactosyltransferase 1 / Beta-1 / 4-GalTase 1 / Beta4Gal-T1 / b4Gal-T1


Mass: 32766.277 Da / Num. of mol.: 1 / Fragment: UNP residues 126-398 / Mutation: R337T, C338T
Source method: isolated from a genetically manipulated source
Details: contains an addition single amino acids Alanine at the N-terminal
Source: (gene. exp.) Homo sapiens (human) / Gene: alpha-lactalbumin, B4GALT1, GGTB2 / Plasmid: pET17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P15291, lactose synthase
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM mes buffer pH 7.0, 12% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 2, 2000 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 14802 / Num. obs: 14000 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rsym value: 0.11 / Net I/σ(I): 10.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.57 / % possible all: 98.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1A4V AND 2AEC

1a4v

2aec


Resolution: 2.7→19.521 Å / SU ML: 0.24 / σ(F): 1.37 / Phase error: 23.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 695 5.03 %
Rwork0.1878 --
obs0.1903 13823 95.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→19.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4165 0 7 31 4203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074274
X-RAY DIFFRACTIONf_angle_d0.845775
X-RAY DIFFRACTIONf_dihedral_angle_d16.2791583
X-RAY DIFFRACTIONf_chiral_restr0.06628
X-RAY DIFFRACTIONf_plane_restr0.003745
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.90810.29171250.26242601X-RAY DIFFRACTION95
2.9081-3.19960.3081520.24322618X-RAY DIFFRACTION96
3.1996-3.660.24871410.19752653X-RAY DIFFRACTION96
3.66-4.60120.21811370.15592624X-RAY DIFFRACTION95
4.6012-19.52140.19031400.15822632X-RAY DIFFRACTION93

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