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

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Basic information

Entry
Database: PDB / ID: 9geg
TitleEntamoeba histolytica Gal/GalNAc lectin heavy chain residues 808-992 in the presence of GalNAc
ComponentsGalactose/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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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: Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1
C: Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9706
Polymers65,3063
Non-polymers6643
Water5,567309
1
A: Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9902
Polymers21,7691
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9902
Polymers21,7691
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9902
Polymers21,7691
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.023, 146.314, 85.095
Angle α, β, γ (deg.)90.000, 113.840, 90.000
Int Tables number5
Space group name H-MC121

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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: 21768.637 Da / Num. of mol.: 3
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: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.62 Å3/Da / Density % sol: 66.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Sodium acetate, pH 4.0, 0.225 M Ammonium sulfate, 12 % w/v PEG 4000, 500 mM GalNAc + 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.85→41.34 Å / Num. obs: 78890 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.999 / Rpim(I) all: 0.035 / Net I/σ(I): 11.5
Reflection shellResolution: 1.85→1.88 Å / Num. unique obs: 3920 / CC1/2: 0.347 / Rpim(I) all: 1.402

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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: 9GEI

9gei


Resolution: 1.85→41.34 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.931 / SU R Cruickshank DPI: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.132 / SU Rfree Blow DPI: 0.124 / SU Rfree Cruickshank DPI: 0.124
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 3814 4.96 %RANDOM
Rwork0.2473 ---
obs0.2484 76821 97.3 %-
Displacement parametersBiso max: 124.42 Å2 / Biso mean: 62 Å2 / Biso min: 32.15 Å2
Baniso -1Baniso -2Baniso -3
1-6.7493 Å20 Å25.451 Å2
2--6.5025 Å20 Å2
3----13.2518 Å2
Refine analyzeLuzzati coordinate error obs: 0.52 Å
Refinement stepCycle: final / Resolution: 1.85→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4398 0 42 309 4749
Biso mean--58.1 59.83 -
Num. residues----544
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1651SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes771HARMONIC5
X-RAY DIFFRACTIONt_it4540HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion627SEMIHARMONIC5
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_contact3443SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4540HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg6139HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion16.49
LS refinement shellResolution: 1.85→1.87 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.6177 79 5.14 %
Rwork0.5329 1458 -
all0.5372 1537 -
obs--51.28 %
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)
15.21090.9320.29850.5043-0.0576-0.36590.1337-0.20510.3847-0.0003-0.08120.1271-0.0377-0.0524-0.0526-0.364-0.0061-0.0128-0.203-0.0431-0.161445.758635.499116.8543
23.0055-2.41060.25132.7494-0.4002-0.3647-0.1154-0.19350.0870.28080.184-0.14030.0518-0.0454-0.0686-0.23970.0719-0.1269-0.3298-0.0542-0.150222.801112.567918.409
30.50461.0751-0.16832.8672-0.2093-0.2206-0.05130.0966-0.11020.11810.114-0.2369-0.0032-0.0236-0.0627-0.2661-0.0098-0.0871-0.37770.0094-0.077854.62714.554822.9749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ C|808 - C|992 }C808 - 992
2X-RAY DIFFRACTION2{ A|808 - A|992 }A808 - 992
3X-RAY DIFFRACTION3{ B|808 - B|992 }B808 - 992

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