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- PDB-6yau: CRYSTAL STRUCTURE OF ASGPR 1 IN COMPLEX WITH GN-A. -

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Basic information

Entry
Database: PDB / ID: 6yau
TitleCRYSTAL STRUCTURE OF ASGPR 1 IN COMPLEX WITH GN-A.
ComponentsAsialoglycoprotein receptor 1
KeywordsSUGAR BINDING PROTEIN / asialog glycoprotein receptor / liver Imaging / NASH
Function / homology
Function and homology information


asialoglycoprotein receptor activity / Asparagine N-linked glycosylation / fucose binding / : / D-mannose binding / receptor-mediated endocytosis / signaling receptor activity / external side of plasma membrane / extracellular region / identical protein binding ...asialoglycoprotein receptor activity / Asparagine N-linked glycosylation / fucose binding / : / D-mannose binding / receptor-mediated endocytosis / signaling receptor activity / external side of plasma membrane / extracellular region / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Hepatic lectin, N-terminal domain / CD209-like, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
Chem-OJB / Asialoglycoprotein receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.397 Å
AuthorsSchreuder, H.A. / Liesum, A.
CitationJournal: Adv Sci / Year: 2020
Title: Triantennary GalNAc Molecular Imaging Probes for Monitoring Hepatocyte Function in a Rat Model of Nonalcoholic Steatohepatitis.
Authors: Mishra, A. / Castaneda, T.R. / Bader, E. / Elshorst, B. / Cummings, S. / Scherer, P. / Bangari, D.S. / Loewe, C. / Schreuder, H. / Poverlein, C. / Helms, M. / Jones, S. / Zech, G. / Licher, ...Authors: Mishra, A. / Castaneda, T.R. / Bader, E. / Elshorst, B. / Cummings, S. / Scherer, P. / Bangari, D.S. / Loewe, C. / Schreuder, H. / Poverlein, C. / Helms, M. / Jones, S. / Zech, G. / Licher, T. / Wagner, M. / Schudok, M. / de Hoop, M. / Plowright, A.T. / Atzrodt, J. / Kannt, A. / Laitinen, I. / Derdau, V.
History
DepositionMar 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Asialoglycoprotein receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5385
Polymers17,9851
Non-polymers5544
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-23 kcal/mol
Surface area6920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.750, 32.530, 39.650
Angle α, β, γ (deg.)90.000, 93.820, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1111-

HOH

21A-1255-

HOH

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Components

#1: Protein Asialoglycoprotein receptor 1 / ASGPR 1 / C-type lectin domain family 4 member H1 / Hepatic lectin H1 / HL-1


Mass: 17984.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASGR1, CLEC4H1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07306
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-OJB / 5-[(2~{R},3~{R},4~{R},5~{R},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-~{N}-[3-(propanoylamino)propyl]pentanamide


Mass: 433.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H35N3O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.05 Å3/Da / Density % sol: 40.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein Buffer: 20 mM Tris-HCl (pH 7.4), 25 mM CaCl2. Reservoir: 100 mM Tris-Hcl (pH 7.5), 28% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99991 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99991 Å / Relative weight: 1
ReflectionResolution: 1.397→57.25 Å / Num. obs: 16299 / % possible obs: 55.7 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 11.1
Reflection shellResolution: 1.397→1.558 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.912 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 815 / CC1/2: 0.593 / Rsym value: 0.912 / % possible all: 10.1

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Processing

Software
NameClassification
XDSdata reduction
BUSTERrefinement
autoPROCdata extraction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dv8

1dv8


Resolution: 1.397→57.25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.11 / SU Rfree Blow DPI: 0.111 / SU Rfree Cruickshank DPI: 0.105
RfactorNum. reflection% reflectionSelection details
Rfree0.219 842 5.16 %RANDOM
Rwork0.172 ---
obs0.175 16299 54.6 %-
Displacement parametersBiso max: 84.53 Å2 / Biso mean: 22.7 Å2 / Biso min: 7.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.2257 Å20 Å2-0.2735 Å2
2---0.1956 Å20 Å2
3----0.0301 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.397→57.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1078 0 25 174 1277
Biso mean--21.1 35.34 -
Num. residues----128
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d398SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes211HARMONIC5
X-RAY DIFFRACTIONt_it1189HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_chiral_improper_torsion134SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies5HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact1492SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1189HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1634HARMONIC21.01
LS refinement shellResolution: 1.397→1.51 Å / Rfactor Rfree error: 0 / Total num. of bins used: 42
RfactorNum. reflection% reflection
Rfree0.2103 19 4.88 %
Rwork0.1994 370 -
all0.1999 389 -
obs--5.75 %

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