[English] 日本語
Yorodumi
- PDB-7jzi: Crystal structure of LAIR1 ectodomain (from MGD21) in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jzi
TitleCrystal structure of LAIR1 ectodomain (from MGD21) in complex with Plasmodium RIFIN (PF3D7_1040300) V2 domain
Components
  • LAIR1 ectodomain from antibody MGD21
  • Rifin
KeywordsIMMUNE SYSTEM / LAIR1 / insertion / antibody / RIFIN / Malaria
Function / homologyVariant surface antigen Rifin / Rifin / membrane => GO:0016020 / : / Rifin
Function and homology information
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.707 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,8226
Polymers52,4324
Non-polymers3902
Water19811
1
A: LAIR1 ectodomain from antibody MGD21
B: Rifin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4113
Polymers26,2162
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-32 kcal/mol
Surface area11730 Å2
MethodPISA
2
C: LAIR1 ectodomain from antibody MGD21
D: Rifin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4113
Polymers26,2162
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-32 kcal/mol
Surface area12280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.409, 72.178, 57.917
Angle α, β, γ (deg.)90.000, 91.080, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain C and resid 109 through 205)
12(chain B and (resid 190 through 231 or resid 233 through 311))
22(chain D and (resid 190 through 231 or resid 233 through 311))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA108 - 205
211(chain C and resid 109 through 205)C109 - 205
112(chain B and (resid 190 through 231 or resid 233 through 311))B190 - 231
122(chain B and (resid 190 through 231 or resid 233 through 311))B233 - 311
212(chain D and (resid 190 through 231 or resid 233 through 311))D190 - 231
222(chain D and (resid 190 through 231 or resid 233 through 311))D233 - 311

NCS ensembles :
ID
1
2

-
Components

#1: Antibody LAIR1 ectodomain from antibody MGD21


Mass: 11088.329 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: 15127.448 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_4895 / Production host: Homo sapiens (human) / References: UniProt: A0A2I0BRG0
#3: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.085 M Na HEPES pH 7.5, 17% PEG 4000, 15% Glycerol, 8.5% Isopropanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0722 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 31123 / % possible obs: 98.8 % / Redundancy: 7.2 % / Biso Wilson estimate: 88.31 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.027 / Rrim(I) all: 0.075 / Χ2: 1.838 / Net I/σ(I): 13.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.755.60.5937680.90.2530.6470.67694.6
2.75-2.86.10.4947870.920.2070.5370.72796.9
2.8-2.856.40.3587870.9680.1470.3880.80799
2.85-2.916.90.3348070.9750.1340.3610.82899
2.91-2.977.10.2788270.9820.110.2990.93899.8
2.97-3.047.30.2637890.9840.1030.2830.96699.7
3.04-3.127.50.2418120.9850.0930.2591.00199.8
3.12-3.27.60.188120.9920.070.1931.25599.8
3.2-3.37.60.1457950.9930.0560.1551.37599.9
3.3-3.47.60.1318300.9940.050.141.424100
3.4-3.527.70.1097960.9930.0420.1171.51299.9
3.52-3.667.60.18170.9930.0380.1071.51100
3.66-3.837.70.0918260.9960.0350.0971.697100
3.83-4.037.60.088040.9960.0310.0861.998100
4.03-4.297.60.0728150.9970.0280.0772.046100
4.29-4.627.60.0678090.9960.0260.0712.038100
4.62-5.087.60.0588320.9970.0230.0632.482100
5.08-5.817.60.0538210.9980.0210.0573.188100
5.81-7.327.50.0548280.9980.0210.0583.815100
7.32-506.60.0537450.9970.0220.0586.32387.3

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
SCALEPACKdata scaling
SOLVEphasing
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.707→44.761 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 35.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2807 3112 10 %
Rwork0.2397 28011 -
obs0.2438 31123 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 280.5 Å2 / Biso mean: 111.112 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.707→44.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3417 0 2 11 3430
Biso mean--276.68 106.01 -
Num. residues----450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083463
X-RAY DIFFRACTIONf_angle_d1.3184685
X-RAY DIFFRACTIONf_chiral_restr0.079550
X-RAY DIFFRACTIONf_plane_restr0.01600
X-RAY DIFFRACTIONf_dihedral_angle_d13.9342109
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A909X-RAY DIFFRACTION15.472TORSIONAL
12C909X-RAY DIFFRACTION15.472TORSIONAL
21B1048X-RAY DIFFRACTION15.472TORSIONAL
22D1048X-RAY DIFFRACTION15.472TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.707-2.74920.36611220.3636104480
2.7492-2.79430.41971390.3605120293
2.7943-2.84250.34731320.3363127397
2.8425-2.89410.53211520.3273132699
2.8941-2.94980.34241430.3123119698
2.9498-3.010.33841340.294131599
3.01-3.07540.36321630.32261308100
3.0754-3.1470.32281340.32281285100
3.147-3.22560.34651550.29491333100
3.2256-3.31280.37271300.29651277100
3.3128-3.41030.31221500.30121333100
3.4103-3.52030.36741470.27761292100
3.5203-3.64610.35951380.28411297100
3.6461-3.7920.23281460.23181313100
3.792-3.96450.34041320.24591307100
3.9645-4.17330.37061520.23331294100
4.1733-4.43460.2791480.20381308100
4.4346-4.77660.26121340.20671301100
4.7766-5.25660.25281370.20811320100
5.2566-6.01570.22161500.19981277100
6.0157-7.57320.23061470.22741315100
7.5732-44.760.21421270.2066109584

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more