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- PDB-9g7d: Crystal structure of ASGPR with bound IMP -

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Basic information

Entry
Database: PDB / ID: 9g7d
TitleCrystal structure of ASGPR with bound IMP
ComponentsAsialoglycoprotein receptor 1
KeywordsSUGAR BINDING PROTEIN / ASIALO GLYCOPROTEIN RECEPTOR / SUGAR BINDING / NATURAL LIGAND COMPLEX / siRNA targeting
Function / homology
Function and homology information


asialoglycoprotein receptor activity / Asparagine N-linked glycosylation / fucose binding / pattern recognition receptor activity / D-mannose binding / receptor-mediated endocytosis / immune response / external side of plasma membrane / extracellular region / metal ion binding ...asialoglycoprotein receptor activity / Asparagine N-linked glycosylation / fucose binding / pattern recognition receptor activity / D-mannose binding / receptor-mediated endocytosis / immune response / external side of plasma membrane / extracellular region / metal ion binding / identical protein 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
INOSINIC ACID / Asialoglycoprotein receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.588 Å
AuthorsSchreuder, H.A. / Hofmeister, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other private Germany
CitationJournal: J.Med.Chem. / Year: 2025
Title: Trivalent siRNA-Conjugates with Guanosine as ASGPR-Binder Show Potent Knock-Down In Vivo.
Authors: Hofmeister, A. / Jahn-Hofmann, K. / Brunner, B. / Helms, M. / Metz-Weidmann, C. / Poeverlein, C. / Zech, G. / Li, Z. / Hessler, G. / Schreuder, H. / Elshorst, B. / Krack, A. / Kurz, M. / ...Authors: Hofmeister, A. / Jahn-Hofmann, K. / Brunner, B. / Helms, M. / Metz-Weidmann, C. / Poeverlein, C. / Zech, G. / Li, Z. / Hessler, G. / Schreuder, H. / Elshorst, B. / Krack, A. / Kurz, M. / Heubel, C. / Scheidler, S.
History
DepositionJul 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)18,4535
Polymers17,9851
Non-polymers4684
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-40 kcal/mol
Surface area6890 Å2
Unit cell
Length a, b, c (Å)113.775, 32.689, 40.819
Angle α, β, γ (deg.)90.00, 91.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1102-

HOH

21A-1162-

HOH

31A-1267-

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-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.11 Å3/Da / Density % sol: 41.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PROTEIN BUFFER: 20 MM TRIS-HCL (PH 7.4), 25 MM CACL2. RESERVOIR: 100 MM TRIS-HCL (PH 7.5), 28% PEG4000, PH 7.50, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.588→56.854 Å / Num. obs: 11473 / % possible obs: 55.7 % / Redundancy: 3.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 7.4
Reflection shellResolution: 1.588→1.862 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.744 / Num. unique obs: 575 / CC1/2: 0.56 / Rsym value: 0.744 / % possible all: 8.2

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Processing

Software
NameVersionClassification
autoPROCdata reduction
XDS(VERSION Jun 1data reduction
STARANISO(Version 1.1.7)data scaling
Aimlessdata scaling
BUSTER2.11.8 (20-OCT-2021)refinement
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.588→56.85 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.19 / SU Rfree Blow DPI: 0.162 / SU Rfree Cruickshank DPI: 0.152
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 581 5.06 %RANDOM
Rwork0.1824 ---
obs0.1848 11473 55.7 %-
Displacement parametersBiso mean: 20.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.3804 Å20 Å2-0.07 Å2
2---0.5162 Å20 Å2
3---0.8966 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.588→56.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1083 0 26 197 1306
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081186HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.841631HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d385SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes209HARMONIC5
X-RAY DIFFRACTIONt_it1186HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.99
X-RAY DIFFRACTIONt_other_torsion17.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion131SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1158SEMIHARMONIC4
LS refinement shellResolution: 1.59→1.78 Å / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.2411 -3.54 %
Rwork0.2606 382 -
all0.2599 396 -
obs--6.57 %

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