[English] 日本語
Yorodumi
- PDB-4bqb: Crystal structure of the FN5 and FN6 domains of NEO1, form 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bqb
TitleCrystal structure of the FN5 and FN6 domains of NEO1, form 2
ComponentsNEOGENINNEO1
KeywordsCELL ADHESION
Function / homology
Function and homology information


negative regulation of axon regeneration / co-receptor binding / BMP receptor binding / regulation of axon regeneration / myoblast fusion / plasma membrane protein complex / positive regulation of BMP signaling pathway / intracellular vesicle / protein secretion / negative regulation of protein secretion ...negative regulation of axon regeneration / co-receptor binding / BMP receptor binding / regulation of axon regeneration / myoblast fusion / plasma membrane protein complex / positive regulation of BMP signaling pathway / intracellular vesicle / protein secretion / negative regulation of protein secretion / axonal growth cone / axon guidance / neuron migration / multicellular organismal-level iron ion homeostasis / cell-cell adhesion / signaling receptor activity / growth cone / intracellular iron ion homeostasis / cadherin binding / neuronal cell body / regulation of DNA-templated transcription / Golgi apparatus / cell surface / nucleoplasm / membrane / plasma membrane
Similarity search - Function
Neogenin, C-terminal / Neogenin C-terminus / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type ...Neogenin, C-terminal / Neogenin C-terminus / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBell, C.H. / Healey, E. / van Erp, S. / Bishop, B. / Tang, C. / Gilbert, R.J.C. / Aricescu, A.R. / Pasterkamp, R.J. / Siebold, C.
CitationJournal: Science / Year: 2013
Title: Structure of the Repulsive Guidance Molecule (Rgm)-Neogenin Signaling Hub
Authors: Bell, C.H. / Healey, E. / Van Erp, S. / Bishop, B. / Tang, C. / Gilbert, R.J.C. / Aricescu, A.R. / Pasterkamp, R.J. / Siebold, C.
History
DepositionMay 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 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 / 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 / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NEOGENIN
B: NEOGENIN
C: NEOGENIN
D: NEOGENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,7728
Polymers116,8874
Non-polymers8854
Water0
1
A: NEOGENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4432
Polymers29,2221
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NEOGENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4432
Polymers29,2221
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NEOGENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4432
Polymers29,2221
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: NEOGENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4432
Polymers29,2221
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.897, 97.394, 91.341
Angle α, β, γ (deg.)90.00, 106.41, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9987, 0.04705, -0.01885), (-0.04815, -0.9968, 0.06327), (-0.01581, 0.06409, 0.9978)31.33, 10.26, 0.5798
2given(0.2235, -0.974, -0.03629), (-0.9743, -0.2244, 0.02159), (-0.02917, 0.03053, -0.9991)17.23, 19.52, 44.11
3given(-0.2472, 0.9685, 0.02856), (0.9655, 0.2487, -0.07768), (-0.08234, 0.008369, -0.9966)14.53, -7.824, 44.97

-
Components

#1: Protein
NEOGENIN / NEO1


Mass: 29221.842 Da / Num. of mol.: 4 / Fragment: FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133
Source method: isolated from a genetically manipulated source
Details: N-LINKED GLYCOSYLATION AT N940 / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: P97798
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / 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
Nonpolymer detailsN-ACETYL-D-GLUCOSAMINE (NAG): N-LINKED GLYCOSYLATION OF NEO1 ASN940

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.13 M POTASSIUM NITRATE, 13% PEG3350, pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97922
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 26660 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 82.22 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.2 / % possible all: 92.7

-
Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.9261 / Cor.coef. Fo:Fc free: 0.9097 / SU R Cruickshank DPI: 1.208 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.816 / SU Rfree Blow DPI: 0.283 / SU Rfree Cruickshank DPI: 0.296
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1337 5.02 %RANDOM
Rwork0.1996 ---
obs0.2008 26625 97.64 %-
Displacement parametersBiso mean: 89.53 Å2
Baniso -1Baniso -2Baniso -3
1-5.5259 Å20 Å20.9268 Å2
2---20.628 Å20 Å2
3---15.1022 Å2
Refine analyzeLuzzati coordinate error obs: 0.468 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6281 0 56 0 6337
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016510HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.138893HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2182SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes127HARMONIC2
X-RAY DIFFRACTIONt_gen_planes927HARMONIC5
X-RAY DIFFRACTIONt_it6510HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion18.27
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion920SEMIHARMONIC5
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_contact7160SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.81 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2543 133 4.69 %
Rwork0.2445 2704 -
all0.245 2837 -
obs--97.64 %
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)
13.17910.6326-2.30846.9079-0.83826.5646-0.4413-0.3231-1.05960.05330.10290.21611.1455-0.01380.3383-0.14350.02230.0938-0.23210.15180.0451-11.241-6.635224.7908
27.75123.7664-3.15258.0893-3.8348.34550.1881-0.39010.1367-0.561-0.8611-0.4808-0.2671.35630.6729-0.23130.02440.0064-0.03370.112-0.176415.545818.17191.6114
35.90712.72260.48376.29742.18715.57210.0246-0.43850.7839-0.2494-0.22070.5078-0.7597-0.2150.1961-0.15630.0488-0.0313-0.2399-0.00890.052242.910116.443424.0164
47.01312.1713.38543.74942.76528.03010.22110.0917-0.2507-0.4578-0.0252-0.08230.6167-0.4428-0.19590.00390.0113-0.0334-0.2-0.0127-0.098415.2714-8.57481.8021
56.98775.6828-3.83319.4652-7.09484.72760.2324-0.07370.49040.2724-0.01660.1528-0.49640.2749-0.2158-0.0269-0.42630.0979-0.0049-0.1666-0.265619.798433.669718.3476
65.23092.3757-2.10567.1867-1.03365.4403-0.1133-1.5668-0.94530.808-0.11370.15090.47340.87870.227-0.3570.12830.03590.35280.5052-0.18172.1590.605242.5453
76.59153.72342.43645.18383.20396.54760.12850.03-0.4544-0.12910.2462-0.38860.7393-0.1771-0.37470.0028-0.1368-0.2065-0.19080.1637-0.18789.0259-25.252618.1518
81.57462.28781.07046.70784.41396.92160.0375-0.2159-0.16330.48840.498-0.76330.01950.2402-0.5354-0.21160.0818-0.14160.1497-0.2126-0.085728.59347.411541.5708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|884 - A|982 }
2X-RAY DIFFRACTION2{ A|983 - A|1083 }
3X-RAY DIFFRACTION3{ B|884 - B|982 }
4X-RAY DIFFRACTION4{ B|983 - B|1083 }
5X-RAY DIFFRACTION5{ C|883 - C|982 }
6X-RAY DIFFRACTION6{ C|983 - C|1083 }
7X-RAY DIFFRACTION7{ D|884 - D|982 }
8X-RAY DIFFRACTION8{ D|983 - D|1085 }

+
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