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Yorodumi- PDB-7jzk: Crystal structure of LAIR1 ectodomain (from MGD21) in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jzk | ||||||
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Title | Crystal structure of LAIR1 ectodomain (from MGD21) in complex with Plasmodium RIFIN (PF3D7_0401300) V2 domain | ||||||
Components |
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Keywords | IMMUNE SYSTEM / LAIR1 / insertion / antibody / RIFIN / Malaria / Plasmodium | ||||||
Function / homology | Variant surface antigen Rifin / Rifin / membrane => GO:0016020 / Rifin Function and homology information | ||||||
Biological species | Homo sapiens (human) Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.457 Å | ||||||
Authors | Xu, K. / Kwong, P.D. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jzk.cif.gz | 102.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jzk.ent.gz | 75.1 KB | Display | PDB format |
PDBx/mmJSON format | 7jzk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jzk_validation.pdf.gz | 755.5 KB | Display | wwPDB validaton report |
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Full document | 7jzk_full_validation.pdf.gz | 761.6 KB | Display | |
Data in XML | 7jzk_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 7jzk_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/7jzk ftp://data.pdbj.org/pub/pdb/validation_reports/jz/7jzk | HTTPS FTP |
-Related structure data
Related structure data | 7jz1C 7jz4C 7jziSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: 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 | 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 | Source method: isolated from a genetically manipulated source #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M NaCl, 0.1 M Tris HCl pH 8.5, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 134.59 Å2 / Biso mean: 54.5714 Å2 / Biso min: 27.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.457→43.17 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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