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- PDB-8ts0: Crystal Structure of human ASGR1 CRD (Carbohydrate Recognition Do... -

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Basic information

Entry
Database: PDB / ID: 8ts0
TitleCrystal Structure of human ASGR1 CRD (Carbohydrate Recognition Domain) bound to 8M24 Fab
Components
  • 8M24 Fab Heavy chain
  • 8M24 Fab Light chain
  • Asialoglycoprotein receptor 1
KeywordsSUGAR BINDING PROTEIN/IMMUNE SYSTEM / ASGR / ASGPR / 8M24 / Endocytosis / SUGAR BINDING PROTEIN / SUGAR BINDING PROTEIN-IMMUNE SYSTEM complex
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
Asialoglycoprotein receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSampathkumar, 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
DepositionAug 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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
H: 8M24 Fab Heavy chain
L: 8M24 Fab Light chain
A: Asialoglycoprotein receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,22912
Polymers68,5573
Non-polymers6739
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-68 kcal/mol
Surface area23650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.911, 90.316, 167.805
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#3: Protein Asialoglycoprotein receptor 1


Mass: 19740.361 Da / Num. of mol.: 1 / Fragment: carbohydrate recognition domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASGR1 / Production host: Homo sapiens (human) / References: UniProt: P07306

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Antibody , 2 types, 2 molecules HL

#1: Antibody 8M24 Fab Heavy chain


Mass: 25327.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 8M24 Fab Light chain


Mass: 23489.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 425 molecules

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


Mass: 92.094 Da / Num. of mol.: 6 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 100mM SPG (succinic acid:sodium dihydrogen phosphate:glycine) buffer pH 9.0, 25% PEG1500, Cryo protectant: 20% 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: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2019
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.7→38.91 Å / Num. obs: 66288 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.03 / Rrim(I) all: 0.107 / Χ2: 0.97 / Net I/σ(I): 14.7 / Num. measured all: 863662
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 2.814 / Num. measured all: 46748 / Num. unique obs: 3439 / CC1/2: 0.407 / Rpim(I) all: 0.789 / Rrim(I) all: 2.923 / Χ2: 0.9 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.14rc1_3177refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→38.047 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2047 3233 4.88 %
Rwork0.1727 --
obs0.1743 66188 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→38.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4345 0 39 416 4800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074561
X-RAY DIFFRACTIONf_angle_d0.876218
X-RAY DIFFRACTIONf_dihedral_angle_d7.4453621
X-RAY DIFFRACTIONf_chiral_restr0.056659
X-RAY DIFFRACTIONf_plane_restr0.005798
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72540.31891520.29492660X-RAY DIFFRACTION100
1.7254-1.75230.32421340.2812690X-RAY DIFFRACTION100
1.7523-1.78110.28181510.26472708X-RAY DIFFRACTION100
1.7811-1.81180.3031380.28122667X-RAY DIFFRACTION100
1.8118-1.84470.29821480.2822730X-RAY DIFFRACTION100
1.8447-1.88020.29391410.25342666X-RAY DIFFRACTION100
1.8802-1.91860.26721520.21912692X-RAY DIFFRACTION100
1.9186-1.96030.22711190.20322750X-RAY DIFFRACTION100
1.9603-2.00590.22741310.18212700X-RAY DIFFRACTION100
2.0059-2.05610.21031130.17462765X-RAY DIFFRACTION100
2.0561-2.11160.22381490.18072646X-RAY DIFFRACTION100
2.1116-2.17380.23631490.18222749X-RAY DIFFRACTION100
2.1738-2.24390.22531320.18232706X-RAY DIFFRACTION100
2.2439-2.32410.21611530.18352703X-RAY DIFFRACTION100
2.3241-2.41720.21411390.18192753X-RAY DIFFRACTION100
2.4172-2.52710.22131270.17332722X-RAY DIFFRACTION100
2.5271-2.66040.21671400.17612759X-RAY DIFFRACTION100
2.6604-2.8270.18511180.18012790X-RAY DIFFRACTION100
2.827-3.04520.2211330.17822746X-RAY DIFFRACTION100
3.0452-3.35150.17941590.16442756X-RAY DIFFRACTION100
3.3515-3.8360.17121400.14852806X-RAY DIFFRACTION100
3.836-4.83140.17181500.13142819X-RAY DIFFRACTION100
4.8314-38.0470.18821650.16142972X-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)
11.27110.27581.01211.9561-1.08711.9107-0.18790.04050.10080.05880.0775-0.0504-0.2220.11180.00010.22860.0305-0.02170.1914-0.0010.234729.683586.071847.0766
20.68260.5214-0.741.1769-0.37631.59410.06630.06370.1104-0.0019-0.01220.1933-0.1052-0.2951-00.304-0.05-0.01680.32440.05090.32269.892187.202617.7388
30.89390.34970.77241.03340.13311.1797-0.10650.0662-0.0744-0.07060.17240.06960.0627-0.0276-00.19050.019-0.00370.21870.02250.228321.343265.658445.5292
41.08280.44350.25221.3613-0.24510.9847-0.06250.179-0.0327-0.49030.0472-0.14140.20970.2048-0.00040.4821-0.05780.01090.32170.05160.313216.755873.863211.0286
51.9632-0.30411.05611.2780.08442.78310.11110.1623-0.02170.0688-0.0221-0.0463-0.03540.18080.00370.15750.0412-0.00020.2059-0.02010.181142.705769.251272.0619
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 125 )
2X-RAY DIFFRACTION2chain 'H' and (resid 126 through 222 )
3X-RAY DIFFRACTION3chain 'L' and (resid 1 through 110 )
4X-RAY DIFFRACTION4chain 'L' and (resid 111 through 212 )
5X-RAY DIFFRACTION5chain 'A' and (resid 153 through 281 )

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