[English] 日本語
Yorodumi
- PDB-6dlf: Crystal structure of NTRI homodimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dlf
TitleCrystal structure of NTRI homodimer
ComponentsNeurotrimin
KeywordsCELL ADHESION / Ig / Complex / Homodimer / Cell Surface / Neuronal
Function / homology
Function and homology information


neuron recognition / Post-translational modification: synthesis of GPI-anchored proteins / cell adhesion / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.446 Å
AuthorsRanaivoson, F.M. / Turk, L.S. / Ozkan, E. / Montelione, G.T. / Comoletti, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1450895 United States
CitationJournal: Structure / Year: 2019
Title: Structure of a heterodimer of neuronal cell surface proteins
Authors: Ranaivoson, F.M. / Turk, L.S. / Ozkan, E. / Montelione, G.T. / Comoletti, D.
History
DepositionJun 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / 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 / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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 2.1Oct 11, 2023Group: Data collection / Database references ...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
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: Neurotrimin
B: Neurotrimin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8477
Polymers67,5372
Non-polymers1,3095
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint10 kcal/mol
Surface area26530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.517, 101.996, 134.025
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Neurotrimin / hNT / IgLON family member 2


Mass: 33768.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTM, IGLON2, NT, UNQ297/PRO337 / Production host: Homo sapiens (human) / References: UniProt: Q9P121
#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: isolated from a genetically manipulated source
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)][b-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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.87 Å3/Da / Density % sol: 68.23 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Na,K-Tartrate, Tris-HCl pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.446→47.664 Å / Num. obs: 14368 / % possible obs: 99.67 % / Redundancy: 6.3 % / CC1/2: 0.998 / Net I/σ(I): 10.7
Reflection shellResolution: 3.45→3.65 Å / Num. unique all: 2254 / CC1/2: 0.758 / Rsym value: 0.951

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DLD

6dld


Resolution: 3.446→47.664 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.08
RfactorNum. reflection% reflectionSelection details
Rfree0.3045 687 4.79 %Random
Rwork0.2735 ---
obs0.275 14353 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.446→47.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 84 0 3468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033536
X-RAY DIFFRACTIONf_angle_d0.7584869
X-RAY DIFFRACTIONf_dihedral_angle_d12.6932120
X-RAY DIFFRACTIONf_chiral_restr0.051610
X-RAY DIFFRACTIONf_plane_restr0.004628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4456-3.71150.37461270.31572649X-RAY DIFFRACTION99
3.7115-4.08480.33281470.28422691X-RAY DIFFRACTION100
4.0848-4.67550.28611250.23972717X-RAY DIFFRACTION100
4.6755-5.88890.25721520.25982739X-RAY DIFFRACTION100
5.8889-47.66850.32371360.28462870X-RAY DIFFRACTION100
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)
17.4880.1974-0.20968.23162.3012.8190.15640.3850.8637-0.3896-0.02460.9948-1.18520.16710.10831.0285-0.1456-0.12741.02410.13620.79442.583632.314-63.0102
23.4748-1.4057-3.54284.1658-1.76759.2528-1.1242-0.5032-1.11271.30890.79530.07280.30240.1610.35271.00090.26440.37021.37430.3341.118-7.24481.8821-34.227
31.91281.35551.13865.7547-1.63841.79680.3689-0.5395-0.36850.1629-1.3710.27371.5573-0.07070.74132.022-0.04340.8041.7337-0.10111.778-16.2917-25.1419-24.8133
41.89721.91252.66218.33471.32064.02280.77740.7583-1.08370.1512-0.85-2.8565-1.95881.5643-0.2361.2717-0.79220.52531.8886-0.51921.364225.782549.4435-53.1271
53.26641.84080.11274.16562.3287.3536-0.11540.3930.1531-1.69951.6328-0.8007-1.64651.34680.82132.0048-0.92460.73632.0613-0.71181.662719.527943.592-62.3456
60.56421.5392.16267.0565.10715.9184-0.26240.5009-0.3653-0.31380.9868-1.33340.36610.38520.28771.1024-0.46110.14730.9879-0.11610.970222.595369.031-24.7042
71.33940.2183-1.14980.0249-0.13980.91671.0032-0.61911.22912.6956-0.74070.4014-0.66350.6887-0.50872.8396-0.2129-0.28151.1309-0.60280.923226.895198.2472-3.1381
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 133 )
2X-RAY DIFFRACTION2chain 'A' and (resid 134 through 210 )
3X-RAY DIFFRACTION3chain 'A' and (resid 211 through 310 )
4X-RAY DIFFRACTION4chain 'B' and (resid 42 through 58 )
5X-RAY DIFFRACTION5chain 'B' and (resid 59 through 124 )
6X-RAY DIFFRACTION6chain 'B' and (resid 125 through 240 )
7X-RAY DIFFRACTION7chain 'B' and (resid 241 through 310 )

+
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://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