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- PDB-7jzk: Crystal structure of LAIR1 ectodomain (from MGD21) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7jzk
TitleCrystal structure of LAIR1 ectodomain (from MGD21) in complex with Plasmodium RIFIN (PF3D7_0401300) V2 domain
Components
  • LAIR1 ecotodomain from MGD21 antibody
  • Rifin
KeywordsIMMUNE SYSTEM / LAIR1 / insertion / antibody / RIFIN / Malaria / Plasmodium
Function / homologyVariant surface antigen Rifin / Rifin / membrane / Rifin
Function and homology information
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.457 Å
AuthorsXu, K. / Kwong, P.D.
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of LAIR1 targeting by polymorphic Plasmodium RIFINs.
Authors: Xu, K. / Wang, Y. / Shen, C.H. / Chen, Y. / Zhang, B. / Liu, K. / Tsybovsky, Y. / Wang, S. / Farney, S.K. / Gorman, J. / Stephens, T. / Verardi, R. / Yang, Y. / Zhou, T. / Chuang, G.Y. / ...Authors: Xu, K. / Wang, Y. / Shen, C.H. / Chen, Y. / Zhang, B. / Liu, K. / Tsybovsky, Y. / Wang, S. / Farney, S.K. / Gorman, J. / Stephens, T. / Verardi, R. / Yang, Y. / Zhou, T. / Chuang, G.Y. / Lanzavecchia, A. / Piccoli, L. / Kwong, P.D.
History
DepositionSep 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 23, 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

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Assembly

Deposited unit
C: LAIR1 ecotodomain from MGD21 antibody
D: Rifin
A: LAIR1 ecotodomain from MGD21 antibody
B: Rifin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7445
Polymers55,1584
Non-polymers5871
Water1,04558
1
C: LAIR1 ecotodomain from MGD21 antibody
D: Rifin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1653
Polymers27,5792
Non-polymers5871
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-3 kcal/mol
Surface area11710 Å2
MethodPISA
2
A: LAIR1 ecotodomain from MGD21 antibody
B: Rifin


Theoretical massNumber of molelcules
Total (without water)27,5792
Polymers27,5792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-7 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.118, 95.839, 71.828
Angle α, β, γ (deg.)90.000, 103.970, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 108 through 205)
21chain C
12(chain B and (resid 195 through 245 or resid 247 through 306))
22(chain D and (resid 195 through 245 or resid 247 through 306))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRLYSLYS(chain A and resid 108 through 205)AC108 - 2051 - 98
211THRTHRLYSLYSchain CCA108 - 2051 - 98
112ALAALASERSER(chain B and (resid 195 through 245 or resid 247 through 306))BD195 - 24516 - 66
122ILEILEALAALA(chain B and (resid 195 through 245 or resid 247 through 306))BD247 - 30668 - 127
212ALAALASERSER(chain D and (resid 195 through 245 or resid 247 through 306))DB195 - 24516 - 66
222ILEILEALAALA(chain D and (resid 195 through 245 or resid 247 through 306))DB247 - 30668 - 127

NCS ensembles :
ID
1
2

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Components

#1: Antibody LAIR1 ecotodomain from MGD21 antibody


Mass: 11847.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Protein Rifin


Mass: 15731.776 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate NF54) (eukaryote)
Strain: isolate NF54 / Gene: CK202_1428, PFNF54_00613 / Production host: Homo sapiens (human) / References: UniProt: W7K133
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M NaCl, 0.1 M Tris HCl pH 8.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 19253 / % possible obs: 92.3 % / Redundancy: 3 % / Biso Wilson estimate: 43.17 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.072 / Rrim(I) all: 0.127 / Χ2: 0.981 / Net I/σ(I): 6.7 / Num. measured all: 57799
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.492.70.4239700.8550.2880.5140.53193.9
2.49-2.542.60.3729500.8960.2760.4670.53291.7
2.54-2.592.90.3359780.950.2340.4110.49792.8
2.59-2.643.30.32710000.920.210.390.53998.2
2.64-2.73.40.29210260.9340.1890.350.53498.8
2.7-2.763.40.2510310.9450.1610.2990.55498.9
2.76-2.833.50.21310240.9640.1350.2530.60998.7
2.83-2.93.40.20610130.9590.1340.2470.60798.4
2.9-2.993.40.18610250.9570.120.2230.65798.3
2.99-3.093.30.16110240.9650.1080.1950.76897.7
3.09-3.23.30.13710030.9650.0920.1650.82997.2
3.2-3.3230.1179960.9680.0820.1440.97897.2
3.32-3.4830.1099790.9660.0770.1341.08794
3.48-3.662.60.0879330.980.0640.1091.23988.7
3.66-3.892.70.0819360.9850.0590.1011.37289.8
3.89-4.192.80.0649210.9920.0460.0791.50487.5
4.19-4.612.50.0578520.9920.0420.0711.7480.9
4.61-5.282.60.0598000.9920.0440.0742.07177.2
5.28-6.652.70.0588950.9920.0410.0721.94584.5
6.65-502.60.068970.9920.0430.0743.00283

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JZI

7jzi


Resolution: 2.457→43.17 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2751 914 4.76 %
Rwork0.2229 18305 -
obs0.2254 19219 91.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.59 Å2 / Biso mean: 54.5714 Å2 / Biso min: 27.88 Å2
Refinement stepCycle: final / Resolution: 2.457→43.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3371 0 39 58 3468
Biso mean--117.73 53.32 -
Num. residues----442
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A908X-RAY DIFFRACTION18.344TORSIONAL
12C908X-RAY DIFFRACTION18.344TORSIONAL
21B906X-RAY DIFFRACTION18.344TORSIONAL
22D906X-RAY DIFFRACTION18.344TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4573-2.58680.36511270.2865256390
2.5868-2.74890.33441510.2499272898
2.7489-2.96110.29361320.2576279698
2.9611-3.2590.26531440.2386279198
3.259-3.73030.29351250.2271259792
3.7303-4.69890.24491220.1995245086
4.6989-43.170.24991130.2006238082

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