[English] 日本語
Yorodumi
- PDB-4l41: Human Lactose synthase: A 2:1 complex between human alpha-lactalb... -

+
Open data


ID or keywords:

Loading...

-
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) / penetration of zona pellucida / Lactose synthesis / regulation of acrosome reaction / Keratan sulfate biosynthesis / lactose synthase / neolactotriaosylceramide beta-1,4-galactosyltransferase ...Defective B4GALT1 causes CDG-2d / galactosyltransferase activity / Interaction With Cumulus Cells And The Zona Pellucida / Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) / penetration of zona pellucida / Lactose synthesis / regulation of acrosome reaction / 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 / N-Glycan antennae elongation / UDP-galactosyltransferase activity / Golgi trans cisterna / macrophage migration / lactose synthase activity / development of secondary sexual characteristics / lactose biosynthetic process / oligosaccharide biosynthetic process / desmosome / galactose metabolic process / acute inflammatory response / positive regulation of epithelial cell proliferation involved in wound healing / Pre-NOTCH Processing in Golgi / binding of sperm to zona pellucida / angiogenesis involved in wound healing / protein N-linked glycosylation / azurophil granule membrane / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi cisterna membrane / beta-tubulin binding / epithelial cell development / alpha-tubulin binding / cytoskeletal protein 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 / cell-cell signaling / lysozyme activity / manganese ion binding / basolateral plasma membrane / defense response to Gram-negative bacterium / cell adhesion / defense response to Gram-positive bacterium / defense response to bacterium / positive regulation of apoptotic process / external side of plasma membrane / Golgi 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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://pdbjlvh1.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