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- PDB-5amo: Structure of a mouse Olfactomedin-1 disulfide-linked dimer of the... -

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Entry
Database: PDB / ID: 5amo
TitleStructure of a mouse Olfactomedin-1 disulfide-linked dimer of the Olfactomedin domain and part of the coiled coil
ComponentsNOELIN
KeywordsSIGNALING PROTEIN / OLFM1 / DISULFIDE / NEUROBIOLOGY / DEVELOPMENT / AMPA RECEPTOR / BETA PROPELLER
Function / homology
Function and homology information


atrioventricular valve formation / neuronal signal transduction / extrinsic component of postsynaptic density membrane / extrinsic component of synaptic membrane / regulation of amyloid-beta formation / cardiac epithelial to mesenchymal transition / regulation of axon extension / negative regulation of amyloid-beta formation / AMPA glutamate receptor complex / positive regulation of epithelial to mesenchymal transition ...atrioventricular valve formation / neuronal signal transduction / extrinsic component of postsynaptic density membrane / extrinsic component of synaptic membrane / regulation of amyloid-beta formation / cardiac epithelial to mesenchymal transition / regulation of axon extension / negative regulation of amyloid-beta formation / AMPA glutamate receptor complex / positive regulation of epithelial to mesenchymal transition / axonal growth cone / synaptic membrane / amyloid-beta binding / perikaryon / positive regulation of apoptotic process / negative regulation of gene expression / axon / neuronal cell body / positive regulation of gene expression / glutamatergic synapse / endoplasmic reticulum / extracellular space / identical protein binding
Similarity search - Function
Noelin domain / Neurogenesis glycoprotein / : / Olfactomedin-like domain / Olfactomedin-like domain / Olfactomedin-like domain profile. / Olfactomedin-like domains / Quinoprotein amine dehydrogenase, beta chain-like / Endoplasmic reticulum targeting sequence.
Similarity search - Domain/homology
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPronker, M.F. / Bos, T.G.A.A. / Sharp, T.H. / Thies-Weesie, D.M. / Janssen, B.J.C.
CitationJournal: J Biol Chem / Year: 2015
Title: Olfactomedin-1 Has a V-shaped Disulfide-linked Tetrameric Structure.
Authors: Matti F Pronker / Trusanne G A A Bos / Thomas H Sharp / Dominique M E Thies-Weesie / Bert J C Janssen /
Abstract: Olfactomedin-1 (Olfm1; also known as noelin and pancortin) is a member of the olfactomedin domain-containing superfamily and a highly expressed neuronal glycoprotein important for nervous system ...Olfactomedin-1 (Olfm1; also known as noelin and pancortin) is a member of the olfactomedin domain-containing superfamily and a highly expressed neuronal glycoprotein important for nervous system development. It binds a number of secreted proteins and cell surface-bound receptors to induce cell signaling processes. Using a combined approach of x-ray crystallography, solution scattering, analytical ultracentrifugation, and electron microscopy we determined that full-length Olfm1 forms disulfide-linked tetramers with a distinctive V-shaped architecture. The base of the "V" is formed by two disulfide-linked dimeric N-terminal domains. Each of the two V legs consists of a parallel dimeric disulfide-linked coiled coil with a C-terminal β-propeller dimer at the tips. This agrees with our crystal structure of a C-terminal coiled-coil segment and β-propeller combination (Olfm1(coil-Olf)) that reveals a disulfide-linked dimeric arrangement with the β-propeller top faces in an outward exposed orientation. Similar to its family member myocilin, Olfm1 is stabilized by calcium. The dimer-of-dimers architecture suggests a role for Olfm1 in clustering receptors to regulate signaling and sheds light on the conformation of several other olfactomedin domain family members.
History
DepositionMar 11, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references / Derived calculations
Revision 1.2Jul 1, 2015Group: Database references
Revision 1.3Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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.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 / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: 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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NOELIN
B: NOELIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,60312
Polymers108,1512
Non-polymers2,45210
Water46826
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)160.220, 43.940, 104.060
Angle α, β, γ (deg.)90.00, 114.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NOELIN / NEURONAL OLFACTOMEDIN-RELATED ER LOCALIZED PROTEIN / OLFACTOMEDIN-1 / PANCORTIN


Mass: 54075.621 Da / Num. of mol.: 2
Fragment: COILED COIL AND OLFACTOMEDIN DOMAIN, RESIDUES 17-478
Source method: isolated from a genetically manipulated source
Details: N-LINKED GLYCOSYLATION ON RESIDUES ASN473, ASN307 AND ASN394
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Organ: BRAIN / Plasmid: PUPE107.03 / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: O88998

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Sugars , 2 types, 6 molecules

#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.: 4
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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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

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Non-polymers , 3 types, 30 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsCORRESPONDS TO UNIPROT ENTRY O88998, BUT WITH MUTATION A329T

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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: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: SITTING DROP AT 293 K, MIXING PROTEIN AT 6 MG/ML 1:1 WITH PRECIPITANT SOLUTION: 1M LICL, 20% PEG6000 (W/V) AND 100 MM TRIS PH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.4→95 Å / Num. obs: 26050 / % possible obs: 98.9 % / Observed criterion σ(I): -4 / Redundancy: 3.4 % / Biso Wilson estimate: 49.62 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.7
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D77

4d77


Resolution: 2.4→50.318 Å / SU ML: 0.33 / σ(F): 1.92 / Phase error: 32.14 / Stereochemistry target values: ML
Details: RESIDUES 17-210, 339-352 AND 478-487 NOT MODELED BECAUSE OF DISORDER OR LIMITED PROTEOLYSIS
RfactorNum. reflection% reflection
Rfree0.2578 2420 5 %
Rwork0.237 --
obs0.238 26030 94.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0.4242 Å2 / ksol: 1.3585 e/Å3
Displacement parametersBiso mean: 69.76 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4119 0 159 26 4304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024396
X-RAY DIFFRACTIONf_angle_d0.5555980
X-RAY DIFFRACTIONf_dihedral_angle_d11.2261555
X-RAY DIFFRACTIONf_chiral_restr0.025664
X-RAY DIFFRACTIONf_plane_restr0.001750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4490.37221340.36242730X-RAY DIFFRACTION95
2.449-2.50230.43031460.34362690X-RAY DIFFRACTION96
2.5023-2.56050.33181420.33692646X-RAY DIFFRACTION94
2.5605-2.62450.38111350.33232690X-RAY DIFFRACTION95
2.6245-2.69550.3521300.33242535X-RAY DIFFRACTION90
2.6955-2.77480.32251410.31612725X-RAY DIFFRACTION96
2.7748-2.86430.34421420.30372689X-RAY DIFFRACTION96
2.8643-2.96670.33781310.29962785X-RAY DIFFRACTION96
2.9667-3.08540.28991450.29432667X-RAY DIFFRACTION95
3.0854-3.22580.31971170.26622639X-RAY DIFFRACTION94
3.2258-3.39590.25371410.25382639X-RAY DIFFRACTION93
3.3959-3.60860.28661650.24172684X-RAY DIFFRACTION96
3.6086-3.88710.22961740.22882673X-RAY DIFFRACTION96
3.8871-4.27810.1961360.19852686X-RAY DIFFRACTION95
4.2781-4.89670.21171420.16732747X-RAY DIFFRACTION95
4.8967-6.16760.19881480.20022687X-RAY DIFFRACTION96
6.1676-50.32860.24111510.20632657X-RAY DIFFRACTION95
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)
15.83294.0936.72579.99255.62947.92020.4786-2.21110.27651.8326-0.76060.8470.8701-2.91520.26630.6939-0.14410.04851.2672-0.05260.749986.123310.39930.3389
25.90360.92480.41922.71370.30814.50750.2050.2551-0.2330.0529-0.0827-0.1353-0.06790.1215-0.10780.2917-0.057-0.02310.4722-0.00980.449964.97768.61124.9528
39.5538-6.98446.70892.1308-8.41072.0268-0.6208-0.640.77621.3958-0.509-0.9618-1.33061.81121.0250.7603-0.2699-0.12811.2714-0.03090.755995.338612.181229.6563
45.73160.66972.92563.00280.2744.4360.153-0.1596-0.10110.1024-0.1614-0.0524-0.0019-0.15960.00070.2926-0.10270.02440.5492-0.04840.4439112.259915.307515.2269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 211 THROUGH 227 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 228 THROUGH 477 ) OR CHAIN 'S' AND (RESID 44)
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 210 THROUGH 227 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 228 THROUGH 480 ) OR CHAIN 'S' AND (RESID 45)

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