[English] 日本語
Yorodumi
- PDB-3zyj: NetrinG1 in complex with NGL1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zyj
TitleNetrinG1 in complex with NGL1
Components
  • LEUCINE-RICH REPEAT-CONTAINING PROTEIN 4C
  • NETRIN-G1
KeywordsCELL ADHESION / SYNAPSE
Function / homology
Function and homology information


laminin complex / : / regulation of neuron projection arborization / basement membrane assembly / Post-translational modification: synthesis of GPI-anchored proteins / synaptic membrane adhesion / regulation of neuron migration / cell-cell adhesion mediator activity / tissue development / regulation of neuron projection development ...laminin complex / : / regulation of neuron projection arborization / basement membrane assembly / Post-translational modification: synthesis of GPI-anchored proteins / synaptic membrane adhesion / regulation of neuron migration / cell-cell adhesion mediator activity / tissue development / regulation of neuron projection development / regulation of axonogenesis / cell adhesion molecule binding / axonogenesis / substrate adhesion-dependent cell spreading / animal organ morphogenesis / modulation of chemical synaptic transmission / cell migration / postsynaptic membrane / membrane => GO:0016020 / glutamatergic synapse / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
Leucine-rich repeat-containing protein 4C / : / Laminin, N-terminal / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) / BspA type Leucine rich repeat region / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai ...Leucine-rich repeat-containing protein 4C / : / Laminin, N-terminal / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) / BspA type Leucine rich repeat region / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / BspA type Leucine rich repeat region (6 copies) / Laminin-type EGF domain / 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 / Laminin / Laminin / Galactose-binding domain-like / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Immunoglobulin I-set / Immunoglobulin I-set domain / Epidermal growth factor-like domain. / Leucine-rich repeat profile. / EGF-like domain profile. / EGF-like domain signature 1. / Leucine-rich repeat / EGF-like domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Leucine-rich repeat domain superfamily / Immunoglobulin V-set domain / Ribbon / Immunoglobulin subtype / Immunoglobulin / Jelly Rolls / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-mannopyranose / alpha-D-mannopyranose / Leucine-rich repeat-containing protein 4C / Netrin-G1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsSeiradake, E. / Coles, C.H. / Perestenko, P.V. / Harlos, K. / McIlhinney, R.A.J. / Aricescu, A.R. / Jones, E.Y.
CitationJournal: Embo J. / Year: 2011
Title: Structural Basis for Cell Surface Patterning Through Netring-Ngl Interactions.
Authors: Seiradake, E. / Coles, C.H. / Perestenko, P.V. / Harlos, K. / Mcilhinney, R.A.J. / Aricescu, A.R. / Jones, E.Y.
History
DepositionAug 23, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Nov 16, 2011Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 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: LEUCINE-RICH REPEAT-CONTAINING PROTEIN 4C
B: NETRIN-G1
C: LEUCINE-RICH REPEAT-CONTAINING PROTEIN 4C
D: NETRIN-G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,40916
Polymers195,1994
Non-polymers2,21012
Water0
1
A: LEUCINE-RICH REPEAT-CONTAINING PROTEIN 4C
B: NETRIN-G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5247
Polymers97,5992
Non-polymers9255
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint3.5 kcal/mol
Surface area35150 Å2
MethodPISA
2
C: LEUCINE-RICH REPEAT-CONTAINING PROTEIN 4C
D: NETRIN-G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8859
Polymers97,5992
Non-polymers1,2857
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-0.4 kcal/mol
Surface area36020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.420, 204.430, 288.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein LEUCINE-RICH REPEAT-CONTAINING PROTEIN 4C / NGL1 / NETRIN-G1 LIGAND / NGL-1


Mass: 49245.578 Da / Num. of mol.: 2 / Fragment: LRR AND IG DOMAINS, 44-444
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK 293 GNTI(-) / Production host: HOMO SAPIENS (human) / References: UniProt: Q9HCJ2
#2: Protein NETRIN-G1 / NETRING1 / LAMINET-1


Mass: 48353.809 Da / Num. of mol.: 2 / Fragment: LAM AND EGF1 DOMAINS, 365-783 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK 293 GNTI(-) / Production host: HOMO SAPIENS (human) / References: UniProt: Q9Y2I2

-
Sugars , 3 types, 10 molecules

#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.: 8
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
#5: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 1 types, 2 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN B, THR 714 TO ALA ENGINEERED RESIDUE IN CHAIN B, THR 717 TO ALA ...ENGINEERED RESIDUE IN CHAIN B, THR 714 TO ALA ENGINEERED RESIDUE IN CHAIN B, THR 717 TO ALA ENGINEERED RESIDUE IN CHAIN D, THR 714 TO ALA ENGINEERED RESIDUE IN CHAIN D, THR 717 TO ALA
Sequence detailsN-TERMINAL SIGNAL SEQUENCE IS CLEAVED DURING PROTEIN PRODUCTION. C-TERMINUS IS FUSED TO 6 X HISTIDINE TAG.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.63 % / Description: NONE
Crystal growDetails: 2% PEG 400, 2 M AMMONIUM SULPHATE, 0.1 M HEPES PH 7.5, ADDITIVE PEG 400.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→29 Å / Num. obs: 39128 / % possible obs: 91.3 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 109.77 Å2 / Rmerge(I) obs: 0.31 / Net I/σ(I): 8.8
Reflection shellResolution: 3.25→3.4 Å / Redundancy: 2.7 % / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 1.5 / % possible all: 73.3

-
Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZYG

3zyg


Resolution: 3.25→29.44 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.8883 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.468
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NAG BMA MAN CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=11252. NUMBER WITH APPROX DEFAULT CCP4 ATOM ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NAG BMA MAN CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=11252. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=134. NUMBER TREATED BY BAD NON- BONDED CONTACTS=2.
RfactorNum. reflection% reflectionSelection details
Rfree0.2683 1967 5.04 %RANDOM
Rwork0.2561 ---
obs0.2567 39036 91.28 %-
Displacement parametersBiso mean: 102.4 Å2
Baniso -1Baniso -2Baniso -3
1--11.7104 Å20 Å20 Å2
2--3.7192 Å20 Å2
3---7.9913 Å2
Refine analyzeLuzzati coordinate error obs: 0.859 Å
Refinement stepCycle: LAST / Resolution: 3.25→29.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11252 0 136 0 11388
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00711655HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9315904HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3843SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes286HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1766HARMONIC5
X-RAY DIFFRACTIONt_it11655HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.49
X-RAY DIFFRACTIONt_other_torsion20.58
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1620SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11983SEMIHARMONIC4
LS refinement shellResolution: 3.25→3.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2767 108 4.77 %
Rwork0.2682 2158 -
all0.2686 2266 -
obs--91.28 %
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)
10.59391.205-0.49661.8409-0.6181.20140.0015-0.05910.0874-0.0274-0.14960.03590.19410.10670.14810.01050.00160.0152-0.1206-0.015-0.1062-0.761880.844464.8516
21.2098-0.5972-0.78632.18891.30921.2369-0.0179-0.0935-0.04160.06490.0186-0.1948-0.17150.0496-0.00070.0925-0.1337-0.0406-0.1090.0387-0.183512.488174.040226.2405
30.86461.23980.51391.47410.84211.9354-0.0409-0.1419-0.08520.0274-0.10710.0034-0.2662-0.08240.148-0.01980.0161-0.0031-0.2111-0.0133-0.0491-0.231121.326352.6377
40.9557-0.78420.7762.2881-0.98651.65420.0763-0.09070.02330.1916-0.06570.13340.0268-0.2168-0.0106-0.1369-0.06290.0831-0.0683-0.0264-0.0427-12.856127.991113.8447
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

+
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