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- PDB-8urf: Crystal Structure of human ASGR2 CRD (Carbohydrate Recognition Do... -

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Basic information

Entry
Database: PDB / ID: 8urf
TitleCrystal Structure of human ASGR2 CRD (Carbohydrate Recognition Domain) bound to 8G8 Fab
Components
  • 8G8 Fab Heavy Chain
  • 8G8 Fab Light Chain
  • Asialoglycoprotein receptor 2
KeywordsSUGAR BINDING PROTEIN / ASGR / ASGPR / ASGR2 / ASGR1 / Fab / 8G8 / AbTAC / LYTAC / Antibody
Function / homology
Function and homology information


asialoglycoprotein receptor activity / Asparagine N-linked glycosylation / fucose binding / endoplasmic reticulum quality control compartment / D-mannose binding / endocytosis / cell surface receptor signaling pathway / external side of plasma membrane / perinuclear region of cytoplasm / 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
Asialoglycoprotein receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSampathumar, P. / Li, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Elife / Year: 2024
Title: Targeted protein degradation systems to enhance Wnt signaling.
Authors: Sampathkumar, P. / Jung, H. / Chen, H. / Zhang, Z. / Suen, N. / Yang, Y. / Huang, Z. / Lopez, T. / Benisch, R. / Lee, S.J. / Ye, J. / Yeh, W.C. / Li, Y.
History
DepositionOct 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 8G8 Fab Light Chain
H: 8G8 Fab Heavy Chain
A: Asialoglycoprotein receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,94012
Polymers67,3243
Non-polymers6169
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.410, 102.410, 358.985
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-407-

CL

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Components

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Protein , 1 types, 1 molecules A

#3: Protein Asialoglycoprotein receptor 2


Mass: 18822.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Human ASGR2 Carbohydrate Recognition Domain (CRD) / Source: (gene. exp.) Homo sapiens (human) / Gene: ASGR2 / Plasmid: pcDNA3.1 / Cell line (production host): Expi293 (HEK293) / Production host: Homo sapiens (human) / References: UniProt: P07307

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Antibody , 2 types, 2 molecules LH

#1: Antibody 8G8 Fab Light Chain


Mass: 23529.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Light chain of Fab-fragment of anti-ASGR1/2 antibody 8G8
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA3.1 / Cell (production host): Expi293 (HEK293) / Production host: Homo sapiens (human)
#2: Antibody 8G8 Fab Heavy Chain


Mass: 24972.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Heavy chain of Fab-fragment of anti-ASGR1/2 antibody 8G8
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA3.1 / Cell (production host): Expi293 (HEK293) / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 267 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.71 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM sodium HEPES pH 7.5, 100mM calcium chloride, 30% (v/v) PEG400 Cryo prodtecion with 16% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 3, 2019 / Details: Double-crystal, Si(111)
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→38.9 Å / Num. obs: 57655 / % possible obs: 100 % / Redundancy: 19.8 % / Biso Wilson estimate: 38.638 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.025 / Rrim(I) all: 0.109 / Net I/σ(I): 16.3
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 20.7 % / Rmerge(I) obs: 3.193 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3681 / CC1/2: 0.44 / Rpim(I) all: 0.718 / Rrim(I) all: 3.273 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14rc1_3177: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→33.544 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2035 2844 4.93 %
Rwork0.166 --
obs0.1679 57636 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→33.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4325 0 34 258 4617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134513
X-RAY DIFFRACTIONf_angle_d1.2256148
X-RAY DIFFRACTIONf_dihedral_angle_d5.4313604
X-RAY DIFFRACTIONf_chiral_restr0.07654
X-RAY DIFFRACTIONf_plane_restr0.008787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93280.31541340.30322766X-RAY DIFFRACTION100
1.9328-1.96790.29031450.25562685X-RAY DIFFRACTION100
1.9679-2.00580.24271260.23682708X-RAY DIFFRACTION100
2.0058-2.04670.28651230.23062708X-RAY DIFFRACTION100
2.0467-2.09120.24361460.21882731X-RAY DIFFRACTION100
2.0912-2.13980.24061670.18862669X-RAY DIFFRACTION100
2.1398-2.19330.22721320.17982708X-RAY DIFFRACTION100
2.1933-2.25260.20391540.16592684X-RAY DIFFRACTION100
2.2526-2.31890.22251420.17842732X-RAY DIFFRACTION100
2.3189-2.39370.21171420.1722731X-RAY DIFFRACTION100
2.3937-2.47930.20781370.17452698X-RAY DIFFRACTION100
2.4793-2.57850.20641490.17822735X-RAY DIFFRACTION100
2.5785-2.69580.25151510.17892736X-RAY DIFFRACTION100
2.6958-2.83790.21921300.17632744X-RAY DIFFRACTION100
2.8379-3.01560.21981450.17722738X-RAY DIFFRACTION100
3.0156-3.24820.21391590.16592724X-RAY DIFFRACTION100
3.2482-3.57480.21381250.15122783X-RAY DIFFRACTION100
3.5748-4.09120.18061300.14812804X-RAY DIFFRACTION100
4.0912-5.15150.17911430.1322801X-RAY DIFFRACTION100
5.1515-330.17351640.17412907X-RAY DIFFRACTION100
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)
13.8878-0.79760.44751.8812-0.20261.53920.08860.1161-0.1012-0.1456-0.1264-0.04080.06090.0926-0.00030.37750.00860.01330.3832-0.03080.35642.32562.6692134.8907
22.6018-1.16370.34091.2566-1.06352.7254-0.2088-0.46690.26820.60430.2587-0.103-0.4549-0.0214-0.00170.5505-0.01950.00790.4403-0.05280.404720.203174.5387159.5825
33.2177-0.61-2.14080.11730.46763.12710.0558-0.4509-0.12270.0788-0.1417-0.079-0.00560.1089-0.00030.3798-0.02170.0070.47110.01730.397354.939360.4523152.1101
41.0707-0.811.30041.76550.49573.4652-0.0131-0.4525-0.3020.18160.2120.3410.0425-0.25760.00070.4829-0.0180.02890.60290.07780.447723.513661.6222168.7301
52.85150.5745-0.48692.9096-0.38942.49670.05580.0852-0.3763-0.0119-0.0085-0.1980.1350.14680.00020.30010.07940.01980.3232-0.04680.375179.2559.2548131.7216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 101 )
2X-RAY DIFFRACTION2chain 'L' and (resid 102 through 211 )
3X-RAY DIFFRACTION3chain 'H' and (resid 2 through 124 )
4X-RAY DIFFRACTION4chain 'H' and (resid 125 through 218 )
5X-RAY DIFFRACTION5chain 'A' and (resid 177 through 304 )

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