[English] 日本語
Yorodumi
- PDB-2r9u: Crystal Structure of Lamprey Variable Lymphocyte Receptor 2913 Ec... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2r9u
TitleCrystal Structure of Lamprey Variable Lymphocyte Receptor 2913 Ectodomain
ComponentsVariable lymphocyte receptor
KeywordsIMMUNE SYSTEM / Adaptive immunity / VLR / Leucine-rich repeat / LRR / Receptor
Function / homology
Function and homology information


Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
Variable lymphocyte receptor
Similarity search - Component
Biological speciesPetromyzon marinus (sea lamprey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHan, B.W. / Herrin, B.R. / Choe, J. / Cooper, M.D. / Wilson, I.A.
CitationJournal: To be Published
Title: Crystal Structure of Lamprey Variable Lymphocyte Receptor 2913 Ectodomain.
Authors: Han, B.W. / Herrin, B.R. / Morris, G.M. / Choe, J. / Cooper, M.D. / Wilson, I.A.
History
DepositionSep 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Variable lymphocyte receptor
B: Variable lymphocyte receptor
C: Variable lymphocyte receptor
D: Variable lymphocyte receptor


Theoretical massNumber of molelcules
Total (without water)77,9644
Polymers77,9644
Non-polymers00
Water5,783321
1
A: Variable lymphocyte receptor


Theoretical massNumber of molelcules
Total (without water)19,4911
Polymers19,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Variable lymphocyte receptor


Theoretical massNumber of molelcules
Total (without water)19,4911
Polymers19,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Variable lymphocyte receptor


Theoretical massNumber of molelcules
Total (without water)19,4911
Polymers19,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Variable lymphocyte receptor


Theoretical massNumber of molelcules
Total (without water)19,4911
Polymers19,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.109, 61.057, 98.081
Angle α, β, γ (deg.)90.000, 107.350, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22A
13D
23A

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 1 / Auth seq-ID: 17 - 190 / Label seq-ID: 1 - 174

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11BB
21AA
12CC
22AA
13DD
23AA

NCS ensembles :
ID
1
2
3
DetailsThe biological assembly is not clear yet.

-
Components

#1: Protein
Variable lymphocyte receptor


Mass: 19490.996 Da / Num. of mol.: 4 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Details: VLR2913 construct in pBAC6 and linearlized DNA ProFold-ER1 (AB Vector) were cotransfected.
Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Plasmid: pBAC6 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): HI 5 / References: UniProt: Q6E4B4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.0-2.4 M NaH2PO4/K2HPO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: MarUSA MarMosaic -325 / Detector: CCD / Date: Jun 3, 2007 / Details: Flat Mirror
RadiationMonochromator: SINGLE CRYSTAL Si(111) BENT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 43844 / % possible obs: 91.3 % / Redundancy: 3.1 % / Rsym value: 0.115 / Net I/σ(I): 9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3 / Num. unique all: 3847 / Rsym value: 0.293 / % possible all: 81.3

-
Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3data extraction
Blu-Icedata collection
MOSFLMdata reduction
HKL-2000data reduction
HKL-2000data scaling
CaspRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O6R

2o6r


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.135 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2232 5.1 %RANDOM
Rwork0.217 ---
obs0.22 41594 91.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.107 Å2
Baniso -1Baniso -2Baniso -3
1-3.91 Å20 Å2-0.36 Å2
2---1.39 Å20 Å2
3----2.73 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5456 0 0 321 5777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0215665
X-RAY DIFFRACTIONr_bond_other_d0.0030.023740
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.9337755
X-RAY DIFFRACTIONr_angle_other_deg1.0683.0079137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3245706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.54325.075268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42315923
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.631528
X-RAY DIFFRACTIONr_chiral_restr0.0960.2872
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026313
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021063
X-RAY DIFFRACTIONr_nbd_refined0.210.21143
X-RAY DIFFRACTIONr_nbd_other0.210.24153
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22838
X-RAY DIFFRACTIONr_nbtor_other0.090.22982
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2318
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.257
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3090.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.226
X-RAY DIFFRACTIONr_mcbond_it1.5424400
X-RAY DIFFRACTIONr_mcbond_other0.31321383
X-RAY DIFFRACTIONr_mcangle_it2.27245715
X-RAY DIFFRACTIONr_scbond_it4.52662498
X-RAY DIFFRACTIONr_scangle_it5.94582033
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B2296TIGHT POSITIONAL0.050.05
1B2296TIGHT THERMAL0.210.5
2C2296TIGHT POSITIONAL0.040.05
2C2296TIGHT THERMAL0.190.5
3D2290TIGHT POSITIONAL0.050.05
3D2290TIGHT THERMAL0.220.5
LS refinement shellResolution: 2.1→2.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 126 -
Rwork0.235 2618 -
all-2744 -
obs--77.95 %
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)
11.48150.72390.56842.824-0.06721.61120.006-0.0217-0.0915-0.02790.0170.05140.0416-0.0584-0.023-0.07880.0057-0.09280.0992-0.00260.085430.01231.86153.502
20.83670.17790.74862.1540.242.8498-0.04460.01710.0386-0.09510.0448-0.0468-0.12530.1473-0.0002-0.0543-0.0151-0.08770.12270.00020.088943.63538.54682.777
31.3983-0.94540.62582.62340.00841.89320.03940.0347-0.0804-0.0067-0.0277-0.02260.09340.0172-0.0117-0.0427-0.0066-0.09850.1065-0.0070.088770.29960.4887.026
40.7301-0.16210.35342.5513-0.81661.5870.0284-0.020.04030.18380.00280.03890.0411-0.0799-0.0312-0.0380.0127-0.08990.1156-0.00770.080456.57166.97357.626
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA17 - 1901 - 174
2X-RAY DIFFRACTION2BB17 - 1901 - 174
3X-RAY DIFFRACTION3CC17 - 1901 - 174
4X-RAY DIFFRACTION4DD17 - 1901 - 174

+
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