[English] 日本語
Yorodumi
- PDB-4u7l: LRIG1 extracellular domain: Structure and Function Analysis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4u7l
TitleLRIG1 extracellular domain: Structure and Function Analysis
ComponentsLeucine-rich repeats and immunoglobulin-like domains protein 1
KeywordsSIGNALING PROTEIN / Stem cell marker / EGFR inhibition
Function / homology
Function and homology information


otolith morphogenesis / hair cycle process / innervation / Signaling by EGFR / extracellular matrix / sensory perception of sound / Negative regulation of MET activity / extracellular space / plasma membrane
Similarity search - Function
Leucine rich repeat C-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily / Alpha-Beta Horseshoe / Immunoglobulin domain ...Leucine rich repeat C-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily / Alpha-Beta Horseshoe / Immunoglobulin domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Immunoglobulin I-set / Immunoglobulin I-set domain / Leucine-rich repeat profile. / Leucine-rich repeat / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Leucine-rich repeat domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
Leucine-rich repeats and immunoglobulin-like domains protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXu, Y.
Funding support Australia, 1items
OrganizationGrant numberCountry
NH&MRC487922 Australia
CitationJournal: J.Mol.Biol. / Year: 2015
Title: LRIG1 Extracellular Domain: Structure and Function Analysis.
Authors: Xu, Y. / Soo, P. / Walker, F. / Zhang, H.H. / Redpath, N. / Tan, C.W. / Nicola, N.A. / Adams, T.E. / Garrett, T.P. / Zhang, J.G. / Burgess, A.W.
History
DepositionJul 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.occupancy / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Leucine-rich repeats and immunoglobulin-like domains protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5987
Polymers50,2531
Non-polymers1,3456
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.940, 93.760, 169.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Leucine-rich repeats and immunoglobulin-like domains protein 1 / LIG-1


Mass: 50253.387 Da / Num. of mol.: 1 / Fragment: LRR repeats, residues 41-494 / Mutation: A42P, A43S, A44R, W69S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRIG1, LIG1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96JA1
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.08 Å3/Da / Density % sol: 60.05 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7 / Details: 16% PEG4000 0.1M Hepes pH7.0 10mM Taurine

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. obs: 28430 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 52.47 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.132 / Rrim(I) all: 0.143 / Χ2: 0.992 / Net I/σ(I): 9.21 / Num. measured all: 202942
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.3-2.390.5752.2420.8722214300530032.41299.9
2.39-2.450.721.8571.0613171179817981.999100
2.45-2.550.7561.3571.5219124260626031.4699.9
2.55-2.730.9070.8822.2527942381438120.9599.9
2.73-2.940.9440.5363.6624598336633640.57799.9
2.94-3.220.9840.3195.8723683325132510.344100
3.22-3.60.9940.14111.821246295629560.153100
3.6-4.150.9970.07420.0917855258025800.081100
4.15-5.080.9980.05924.2615116226922680.064100
5.08-7.140.9980.05624.7111737176717670.061100
7.140.9970.04527.276256108410280.0594.8

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
PHASERphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XKU

1xku


Resolution: 2.3→48.378 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2478 1387 4.89 %RANDOM
Rwork0.1942 26998 --
obs0.1968 28385 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 208.07 Å2 / Biso mean: 72.614 Å2 / Biso min: 36 Å2
Refinement stepCycle: final / Resolution: 2.3→48.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3524 0 85 34 3643
Biso mean--101.07 59.47 -
Num. residues----454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043686
X-RAY DIFFRACTIONf_angle_d0.8864975
X-RAY DIFFRACTIONf_chiral_restr0.032589
X-RAY DIFFRACTIONf_plane_restr0.004633
X-RAY DIFFRACTIONf_dihedral_angle_d13.3941354
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.38220.4331250.369726022727100
2.3822-2.47750.39421480.327226532801100
2.4775-2.59030.3141550.287126682823100
2.5903-2.72680.34061350.253226362771100
2.7268-2.89770.28981380.241526792817100
2.8977-3.12140.32071390.25526832822100
3.1214-3.43540.31221250.223927102835100
3.4354-3.93230.22961390.163227542893100
3.9323-4.95350.17831380.143827472885100
4.9535-48.38870.21151450.16492866301198
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)
15.85281.81720.35846.73940.74196.45790.4183-1.2482-0.53681.039-0.081-0.71750.87222.2961-0.23120.93020.0948-0.19031.44850.11590.759521.36445.512523.9591
22.8010.12951.30753.1816-0.16056.59210.126-0.6712-0.00290.5798-0.15070.03990.1722-0.2643-0.0220.5444-0.13160.03630.58830.03870.32584.409710.099513.1699
32.68180.16640.82358.05951.27545.9150.1486-0.37570.02870.1417-0.23560.24910.136-0.23960.06840.41160.01690.01730.6576-0.01150.2925-3.94539.2035-6.4882
40.8718-1.1603-1.0224.34011.8684.58940.08180.2674-0.0335-0.4054-0.1160.3225-0.3864-0.37470.00670.4308-0.0198-0.06270.67610.02410.3987-1.00293.8203-22.7236
52.2962-1.8267-1.22884.34983.14824.50640.27490.312-0.115-0.30230.0072-0.21170.03430.1234-0.27120.4979-0.0688-0.05730.8388-0.10580.430513.2015-10.8496-38.9984
62.68670.48860.63793.45682.52767.06510.03160.1525-0.33050.46710.8569-0.581.01930.9791-0.70910.68690.1554-0.26840.8645-0.24810.84321.5704-27.0501-45.2244
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 1 through 34 )A1 - 34
2X-RAY DIFFRACTION2chain A and (resid 35 through 159 )A35 - 159
3X-RAY DIFFRACTION3chain A and (resid 160 through 206 )A160 - 206
4X-RAY DIFFRACTION4chain A and (resid 207 through 302 )A207 - 302
5X-RAY DIFFRACTION5chain A and (resid 303 through 417 )A303 - 417
6X-RAY DIFFRACTION6chain A and (resid 418 through 455 )A418 - 455

+
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