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- PDB-9gei: Entamoeba histolytica Gal/GalNAc lectin heavy chain residues 808-... -

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Basic information

Entry
Database: PDB / ID: 9gei
TitleEntamoeba histolytica Gal/GalNAc lectin heavy chain residues 808-992 in the presence of monoclonal antibody CP33-H/L-LA22
Components
  • CP33-H/L-LA22
  • Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1
KeywordsCELL ADHESION / Entamoeba histolytica / lectin / Gal/GalNAc / trogocytosis
Function / homologycarbohydrate binding / cell adhesion / plasma membrane / Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1
Function and homology information
Biological speciesEntamoeba histolytica (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.034 Å
AuthorsGerard, S.F. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: Structural basis for carbohydrate recognition by the Gal/GalNAc lectin of Entamoeba histolytica
Authors: Gerard, S.F. / Higgins, M.K.
History
DepositionAug 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1
B: CP33-H/L-LA22
C: Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1
D: CP33-H/L-LA22


Theoretical massNumber of molelcules
Total (without water)97,0764
Polymers97,0764
Non-polymers00
Water00
1
A: Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1
B: CP33-H/L-LA22


Theoretical massNumber of molelcules
Total (without water)48,5382
Polymers48,5382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1
D: CP33-H/L-LA22


Theoretical massNumber of molelcules
Total (without water)48,5382
Polymers48,5382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.099, 151.982, 60.295
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1 / Gal/GalNAc lectin heavy subunit 1 / Galactose-inhibitable lectin 170 kDa subunit / N-acetyl D- ...Gal/GalNAc lectin heavy subunit 1 / Galactose-inhibitable lectin 170 kDa subunit / N-acetyl D-galactosamine-specific lectin


Mass: 21713.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: hgl1, EHI_133900 / Production host: Homo sapiens (human) / References: UniProt: P32022
#2: Antibody CP33-H/L-LA22


Mass: 26824.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: 3.24 Å3/Da / Density % sol: 62.09 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Potassium chloride, 0.1M Bis-Tris, pH 6.0, 18%w/v PEG4000, 20 mM GalNAc +20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.85506 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Aug 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85506 Å / Relative weight: 1
ReflectionResolution: 3.03→75.99 Å / Num. obs: 16151 / % possible obs: 92.7 % / Redundancy: 12.8 % / CC1/2: 0.991 / Rpim(I) all: 0.093 / Net I/σ(I): 6.6
Reflection shellResolution: 3.03→3.39 Å / Num. unique obs: 808 / CC1/2: 0.702 / Rpim(I) all: 0.468

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (26-JUL-2023)refinement
PDB_EXTRACT3.28data extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8RZ0

8rz0


Resolution: 3.034→75.99 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.867 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.591
RfactorNum. reflection% reflectionSelection details
Rfree0.277 779 4.82 %RANDOM
Rwork0.2415 ---
obs0.2432 16151 65.6 %-
Displacement parametersBiso max: 178.93 Å2 / Biso mean: 100.82 Å2 / Biso min: 61.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.3893 Å20 Å20 Å2
2--1.1819 Å20 Å2
3----0.7926 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: final / Resolution: 3.034→75.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6268 0 0 0 6268
Num. residues----800
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2206SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1088HARMONIC5
X-RAY DIFFRACTIONt_it6414HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion854SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4471SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6414HARMONIC20.006
X-RAY DIFFRACTIONt_angle_deg8692HARMONIC20.85
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion20.1
LS refinement shellResolution: 3.034→3.28 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3257 31 7.28 %
Rwork0.3106 395 -
obs--8.41 %
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)
10.06260.84710.80743.40732.52042.91340.2217-0.11390.09920.2491-0.45090.16290.0804-0.21420.22920.0863-0.1494-0.02410.04180.06420.185-39.0514.1966-57.5991
25.10040.4142.16555.9651.0853.5497-0.56310.77270.6121-0.83830.03780.48130.4980.46540.52540.0234-0.1833-0.22840.03520.2113-0.0924-44.47622.7201-89.3681
31.79571.25380.02044.0428-0.14610.46710.0547-0.0440.05340.3847-0.1475-0.21940.22870.01250.09280.26390.06130.06560.01510.0508-0.0364-32.9862-24.1729-54.5815
45.8468-0.2289-3.23095.64851.72893.32220.30540.0965-0.66820.3751-0.59580.97450.2121-0.35420.29040.0504-0.26410.304-0.1323-0.2797-0.007-65.3606-34.2059-51.9895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A808 - 992
2X-RAY DIFFRACTION2{ B|* }B4 - 248
3X-RAY DIFFRACTION3{ C|* }C808 - 992
4X-RAY DIFFRACTION4{ D|* }D4 - 248

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