[English] 日本語
Yorodumi
- PDB-2xot: Crystal structure of neuronal leucine rich repeat protein AMIGO-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xot
TitleCrystal structure of neuronal leucine rich repeat protein AMIGO-1
ComponentsAmphoterin-induced protein 1
KeywordsCELL ADHESION / NEURONAL PROTEIN / NEURITE GROWTH REGULATION
Function / homology
Function and homology information


pericellular basket / positive regulation of voltage-gated potassium channel activity / neuron projection fasciculation / cellular response to L-glutamate / positive regulation of potassium ion transmembrane transport / axonal fasciculation / positive regulation of synapse assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / positive regulation of axonogenesis / neuronal cell body membrane ...pericellular basket / positive regulation of voltage-gated potassium channel activity / neuron projection fasciculation / cellular response to L-glutamate / positive regulation of potassium ion transmembrane transport / axonal fasciculation / positive regulation of synapse assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / positive regulation of axonogenesis / neuronal cell body membrane / homophilic cell adhesion via plasma membrane adhesion molecules / plasma membrane => GO:0005886 / potassium channel regulator activity / myelination / axonogenesis / brain development / positive regulation of neuron projection development / perikaryon / membrane => GO:0016020 / cell adhesion / neuronal cell body / dendrite
Similarity search - Function
Amphoterin-induced protein / Amphoterin-induced protein 1 / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-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 ...Amphoterin-induced protein / Amphoterin-induced protein 1 / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-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 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Amphoterin-induced protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKajander, T. / Kuja-Panula, J. / Rauvala, H. / Goldman, A.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal Structure and Role of Glycans and Dimerisation in Folding of Neuronal Leucine-Rich Repeat Protein Amigo-1
Authors: Kajander, T. / Kuja-Panula, J. / Rauvala, H. / Goldman, A.
History
DepositionAug 23, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references
Revision 1.2Oct 19, 2011Group: Database references
Revision 1.3Nov 23, 2011Group: Database references
Revision 1.4Jun 6, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_seq_type / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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.auth_asym_id / _atom_site.auth_seq_id ..._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_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Amphoterin-induced protein 1
B: Amphoterin-induced protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6534
Polymers82,4802
Non-polymers1,1732
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-5.6 kcal/mol
Surface area31020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.440, 74.630, 87.270
Angle α, β, γ (deg.)90.00, 98.66, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A33 - 365
2115B33 - 365

NCS oper: (Code: given
Matrix: (-0.9366, 0.3493, -0.0268), (0.3497, 0.9368, -0.0131), (0.0205, -0.0217, -0.9996)
Vector: 5.6005, 0.3372, 86.2633)

-
Components

#1: Antibody Amphoterin-induced protein 1 / AMIGO-1 / Alivin-2


Mass: 41239.777 Da / Num. of mol.: 2 / Fragment: LRR AND IG DOMAINS, RESIDUES 28-372
Source method: isolated from a genetically manipulated source
Details: N-GLYCOSYLATED AT ASN72 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Amigo1, Ali2, Amigo, Kiaa1163 / Plasmid: MODIFIED PRMHA3 / Cell line (production host): S2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q80ZD8
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONSTRUCT CONTAINS FEW ADDITIONAL N-TERMINAL AMINO ACIDS FROM THE VECTOR AND A C-TERMINAL STREPII ...CONSTRUCT CONTAINS FEW ADDITIONAL N-TERMINAL AMINO ACIDS FROM THE VECTOR AND A C-TERMINAL STREPII TAG. SOME RESIDUES ARE TRUNCATED TO ALA.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.43 % / Description: NONE
Crystal growpH: 6.5 / Details: 1.6 M MGSO4, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 27, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 52608 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.5
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.7 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
PHASERmodel building
XDSdata scaling
SHELXphasing
SHARPphasing
DMphasing
PHASERphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2→29.1 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.916 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25541 2624 5 %RANDOM
Rwork0.20786 ---
obs0.2102 49850 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.875 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.18 Å2
2---0.06 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5078 0 78 388 5544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225295
X-RAY DIFFRACTIONr_bond_other_d0.0010.023326
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.9687245
X-RAY DIFFRACTIONr_angle_other_deg0.9563.0058150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7425661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.14225.198227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80215799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.7631512
X-RAY DIFFRACTIONr_chiral_restr0.0850.2862
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025869
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021015
X-RAY DIFFRACTIONr_nbd_refined0.2380.21103
X-RAY DIFFRACTIONr_nbd_other0.2090.23540
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22532
X-RAY DIFFRACTIONr_nbtor_other0.0850.22738
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2374
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2690.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1830.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8511.53591
X-RAY DIFFRACTIONr_mcbond_other0.1931.51320
X-RAY DIFFRACTIONr_mcangle_it1.26825313
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.89432146
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.764.51932
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1805medium positional0.940.5
2B1805medium positional0.940.5
1A2082loose positional1.125
2B2082loose positional1.125
1A1805medium thermal1.182
2B1805medium thermal1.182
1A2082loose thermal1.6110
2B2082loose thermal1.6110
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 194 -
Rwork0.288 3667 -
obs--100 %

+
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