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- PDB-5jq1: Efficient targeting of the asialoglycoprotein receptor by polyval... -

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Basic information

Entry
Database: PDB / ID: 5jq1
TitleEfficient targeting of the asialoglycoprotein receptor by polyvalent display of a compact galactosamine mimic
ComponentsAsialoglycoprotein receptor 1
KeywordsSUGAR BINDING PROTEIN / asialoglycoprotein receptor / carbohydrates / liver 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. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like ...Hepatic lectin, N-terminal domain / CD209-like, C-type lectin-like domain / : / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-ZPF / Asialoglycoprotein receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsLiu, S.
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Efficient Liver Targeting by Polyvalent Display of a Compact Ligand for the Asialoglycoprotein Receptor.
Authors: Sanhueza, C.A. / Baksh, M.M. / Thuma, B. / Roy, M.D. / Dutta, S. / Preville, C. / Chrunyk, B.A. / Beaumont, K. / Dullea, R. / Ammirati, M. / Liu, S. / Gebhard, D. / Finley, J.E. / Salatto, C. ...Authors: Sanhueza, C.A. / Baksh, M.M. / Thuma, B. / Roy, M.D. / Dutta, S. / Preville, C. / Chrunyk, B.A. / Beaumont, K. / Dullea, R. / Ammirati, M. / Liu, S. / Gebhard, D. / Finley, J.E. / Salatto, C.T. / King-Ahmad, A. / Stock, I. / Atkinson, K. / Reidich, B. / Lin, W. / Kumar, R. / Tu, M. / Menhaji-Klotz, E. / Price, D.A. / Liras, S. / Finn, M.G. / Mascitti, V.
History
DepositionMay 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Asialoglycoprotein receptor 1
B: Asialoglycoprotein receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,76511
Polymers34,0232
Non-polymers7429
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-82 kcal/mol
Surface area12880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.080, 59.490, 68.650
Angle α, β, γ (deg.)90.00, 93.18, 90.00
Int Tables number4
Space group name H-MP1211

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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: 17011.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASGR1, CLEC4H1
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P07306
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZPF / N-[(1S,2R,3R,4R,5S)-2,3-dihydroxy-1-(hydroxymethyl)-6,8-dioxabicyclo[3.2.1]octan-4-yl]acetamide


Mass: 233.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15NO6
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
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: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M cacodylate, pH 6.8-7.4, 0.1-0.2M (NH4)2SO4, 14-20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→34.37 Å / Num. obs: 29063 / % possible obs: 88.8 % / Biso Wilson estimate: 28.39 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.8
Reflection shellResolution: 1.83→1.93 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4276 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DV8

1dv8


Resolution: 1.83→34.37 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.119 / SU Rfree Blow DPI: 0.115 / SU Rfree Cruickshank DPI: 0.115
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1480 5.09 %RANDOM
Rwork0.187 ---
obs0.189 29063 99.2 %-
Displacement parametersBiso mean: 31.45 Å2
Baniso -1Baniso -2Baniso -3
1-4.893 Å20 Å21.2689 Å2
2---7.3541 Å20 Å2
3---2.4612 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 1.83→34.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 39 146 2348
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012320HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.93208HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d750SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes70HARMONIC2
X-RAY DIFFRACTIONt_gen_planes331HARMONIC5
X-RAY DIFFRACTIONt_it2320HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.85
X-RAY DIFFRACTIONt_other_torsion17.48
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion260SEMIHARMONIC5
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_contact2646SEMIHARMONIC4
LS refinement shellResolution: 1.83→1.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.245 157 5.48 %
Rwork0.205 2709 -
all0.207 2866 -
obs--99.27 %
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)
11.81680.22110.07240.5096-0.02612.4464-0.01790.1419-0.0558-0.06860.02760.00430.1751-0.0843-0.0097-0.0258-0.00070.0128-0.06270.01-0.04221.7810.472725.6175
21.668-0.28350.82521.0323-0.47492.5322-0.0585-0.22960.17270.10810.01160.0322-0.103-0.05970.047-0.05610.01570.0242-0.0096-0.0154-0.0575-16.5639-0.587450.9897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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