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- PDB-4bqb: Crystal structure of the FN5 and FN6 domains of NEO1, form 2 -

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Basic information

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


trans-synaptic signaling, modulating synaptic transmission / negative regulation of axon regeneration / co-receptor binding / BMP receptor binding / regulation of axon regeneration / plasma membrane protein complex / positive regulation of BMP signaling pathway / myoblast fusion / intracellular vesicle / protein secretion ...trans-synaptic signaling, modulating synaptic transmission / negative regulation of axon regeneration / co-receptor binding / BMP receptor binding / regulation of axon regeneration / plasma membrane protein complex / positive regulation of BMP signaling pathway / myoblast fusion / intracellular vesicle / protein secretion / negative regulation of protein secretion / postsynaptic density membrane / multicellular organismal-level iron ion homeostasis / signaling receptor activity / growth cone / intracellular iron ion homeostasis / cell adhesion / cadherin binding / regulation of DNA-templated transcription / glutamatergic synapse / cell surface / Golgi apparatus / nucleoplasm / membrane / plasma membrane
Similarity search - Function
Neogenin, C-terminal / Neogenin C-terminus / 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. ...Neogenin, C-terminal / Neogenin C-terminus / 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 / Immunoglobulin-like fold / Immunoglobulins / 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
Revision 1.5Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water00
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

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Components

#1: Protein
NEOGENIN


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-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: 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
Has protein modificationY
Nonpolymer detailsN-ACETYL-D-GLUCOSAMINE (NAG): N-LINKED GLYCOSYLATION OF NEO1 ASN940

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Experimental details

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Experiment

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

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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

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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

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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 }

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