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- PDB-6qm3: Crystal structure of a calcium- and sodium-bound mouse Olfactomed... -

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Basic information

Entry
Database: PDB / ID: 6qm3
TitleCrystal structure of a calcium- and sodium-bound mouse Olfactomedin-1 disulfide-linked dimer of the Olfactomedin domain and part of coiled coil
ComponentsNoelin
KeywordsSIGNALING PROTEIN / Calcium / Beta-propeller / Secreted / Brain
Function / homology
Function and homology information


extrinsic component of synaptic membrane / atrioventricular valve formation / neuronal signal transduction / extrinsic component of postsynaptic density membrane / cardiac epithelial to mesenchymal transition / regulation of axon extension / AMPA glutamate receptor complex / axonal growth cone / positive regulation of epithelial to mesenchymal transition / synaptic membrane ...extrinsic component of synaptic membrane / atrioventricular valve formation / neuronal signal transduction / extrinsic component of postsynaptic density membrane / cardiac epithelial to mesenchymal transition / regulation of axon extension / AMPA glutamate receptor complex / axonal growth cone / positive regulation of epithelial to mesenchymal transition / synaptic membrane / perikaryon / positive regulation of apoptotic process / axon / negative regulation of gene expression / neuronal cell body / glutamatergic synapse / positive regulation of gene expression / signal transduction / endoplasmic reticulum / extracellular space
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
ACETATE ION / CACODYLATE ION / Noelin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPronker, M.F. / van den Hoek, H.G. / Janssen, B.J.C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research723.012.002 Netherlands
CitationJournal: BMC Mol Cell Biol / Year: 2019
Title: Design and structural characterisation of olfactomedin-1 variants as tools for functional studies.
Authors: Pronker, M.F. / van den Hoek, H. / Janssen, B.J.C.
History
DepositionFeb 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_chem_comp_identifier / 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 / _citation.country / _entity.pdbx_description / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.conn_type_id / _struct_conn.id / _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_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Noelin
B: Noelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,75118
Polymers63,5412
Non-polymers2,21016
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, as confirmed by non-reducing SDS-PAGE
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-35 kcal/mol
Surface area23390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.705, 46.971, 104.952
Angle α, β, γ (deg.)90.000, 117.435, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein / Sugars , 2 types, 10 molecules AB

#1: Protein Noelin / Neuronal olfactomedin-related ER localized protein / Olfactomedin-1 / Pancortin


Mass: 31770.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Olfm1, Noe1, Noel, Noel1 / Plasmid: pUPE107.03
Details (production host): Cystatin secretion signal and C-terminal His6-tag
Cell line (production host): HEK293 GntI-/- / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: O88998
#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.: 8 / Source method: obtained synthetically / 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 , 5 types, 107 molecules

#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.08 M Mg Acetate, 30% PEG4000, 0.05 M Na Cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.89→75.994 Å / Num. obs: 29117 / % possible obs: 92.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 34.574240918 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.039 / Rrim(I) all: 0.072 / Net I/σ(I): 10.3
Reflection shellResolution: 1.891→2.101 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1457 / CC1/2: 0.551 / Rpim(I) all: 0.479 / Rrim(I) all: 0.893 / % possible all: 77.2

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.12_2829refinement
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AMO

5amo


Resolution: 2→71.3 Å / SU ML: 0.214022057126 / Cross valid method: FREE R-VALUE / σ(F): 1.34348608369 / Phase error: 28.6783724053
RfactorNum. reflection% reflection
Rfree0.215627701203 1459 5.09623109434 %
Rwork0.178664702636 --
obs0.180557826647 27170 60.2576245501 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.0864676127 Å2
Refinement stepCycle: LAST / Resolution: 2→71.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4321 0 133 99 4553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006544724077174582
X-RAY DIFFRACTIONf_angle_d0.8523179114626243
X-RAY DIFFRACTIONf_chiral_restr0.0638063696724671
X-RAY DIFFRACTIONf_plane_restr0.00414724978879794
X-RAY DIFFRACTIONf_dihedral_angle_d12.66035694891629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.07150.272323987722270.263594669874627X-RAY DIFFRACTION13.9356488387
2.0715-2.15450.371946703554530.27094397272888X-RAY DIFFRACTION19.9491202035
2.1545-2.25250.278226155618740.2641568911251190X-RAY DIFFRACTION26.7117497887
2.2525-2.37130.304686349063660.2717076694791514X-RAY DIFFRACTION33.6027222459
2.3713-2.51990.2836299877611070.2766915970742035X-RAY DIFFRACTION45.4970263381
2.5199-2.71450.3017279007271650.2680019703773083X-RAY DIFFRACTION68.9303904924
2.7145-2.98760.2632113412792270.233971756844291X-RAY DIFFRACTION94.7567114094
2.9876-3.41990.2301712334322340.1920240965564478X-RAY DIFFRACTION99.2626922267
3.4199-4.30870.1732552269352670.1476137131424455X-RAY DIFFRACTION98.662766402
4.3087-71.36090.1937768388642390.1384008643814609X-RAY DIFFRACTION98.4365482234
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)
10.8265893789940.4327943036070.2073120014910.212746328926-0.1237959881822.319253109730.449709575714-0.697572300858-0.2817723526540.202089253649-0.233353624567-0.270089139768-0.04379277952410.691146984591-0.2104496272990.356377227505-0.167638513677-0.0005110979089860.5129357465920.008866480936140.55282352224951.534379717811.262113373971.9864801153
22.711369694412.93927562105-0.4957033849444.025011096671.580098959325.149979583860.376656279935-1.27745261655-0.6587083121930.667913846202-0.210588228011-0.5780048431540.287307911989-0.0181530867682-0.1287432058050.398916299872-0.175858969067-0.08563466509110.6654371488690.08758284278380.31327304852540.3758490649.0175421570281.8477756595
33.10923147431-1.19814500101-0.3140417522144.457808954262.089867456984.374994880720.195531587586-1.26883001504-0.7431093639181.251791087640.1155507227510.0720834541584-0.0988410453804-0.470949819071-0.1451907286880.47909664277-0.2392575117040.01557193890240.87853033573-0.0951858317877-0.036811966647233.700744293313.299983697183.813045735
42.297121525760.6035735349921.685653419342.60265644715-0.220311900384.000476195450.35288902026-1.819146173360.8567025005880.7242631188060.005115670169330.357006133901-1.082245479810.0330600670520.9025066920220.452207649001-0.2625776064630.07047176522990.816630790717-0.3127169289540.18933059393438.406768644522.789002939181.9383204809
52.26238115071-0.108755518810.3707174980421.458803266220.7731860930623.568992965620.077710675434-0.5069732023481.00175967335-0.04975199504-0.1443433149260.0939864525145-1.05980690359-0.03979834718320.2015061668350.537468598741-0.1063964057940.0926767713980.306703551946-0.1221964131430.45086837776138.154329143226.381123903769.964038939
66.19330806315-0.737670861477-0.2030801997853.716366561150.3275362800983.471330598270.1941511532950.5328387785510.421787141811-0.142659473236-0.0849504393652-0.221503722349-0.6278273552280.312815096955-0.0308124778160.32617183108-0.08091012240570.0326604294150.2517803206090.02463278539160.18872079700243.348533603920.531943744159.0210688396
73.867926026540.928558605637-0.2673299956813.28162832621-0.5866313444154.384250099030.175559805189-0.1069045396-0.9801434676050.0277852004412-0.292786537799-0.5411765995580.1205120336860.4895877637410.07694337284760.247600803006-0.0489933682893-0.059698064770.245344356097-0.01831116953560.37600323328643.93250985027.1879467923566.070229217
85.506872427590.7698693266021.780344668351.626393341220.1784613618913.507874843780.299481139397-0.722864773127-0.3045120742170.0823310567279-0.256908632887-0.04942633586410.08784388673140.06141336142430.05537142799940.301012589122-0.158279433387-0.006509940736790.3218031816130.0460731236860.33371812065391.404224284324.090365337468.4599440027
93.78390127981-0.5362972283511.036555935383.829888414020.7594139482214.519612671960.181672310470.142001750483-0.313154959432-0.140696339413-0.17770158744-0.4015662104060.1135814412030.1938756290860.0558691517020.273920185187-0.127064357608-0.05007981951930.171344626490.04005452488840.3848757139884.096384839417.366052091854.3748523904
104.808157139792.381491564790.9085525472453.13787420473-0.1017644784362.12741729908-0.361809513906-0.3325881058080.716369560198-0.2845310156880.05708085300870.392080854249-0.906230885437-0.001739667340950.03694711251510.472600773317-0.136064504842-0.05720157749920.134091648512-0.02735084065440.37266658918284.595374538732.858142798458.045576876
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 212 through 246 )
2X-RAY DIFFRACTION2chain 'A' and (resid 247 through 285 )
3X-RAY DIFFRACTION3chain 'A' and (resid 286 through 303 )
4X-RAY DIFFRACTION4chain 'A' and (resid 304 through 328 )
5X-RAY DIFFRACTION5chain 'A' and (resid 329 through 388 )
6X-RAY DIFFRACTION6chain 'A' and (resid 389 through 437 )
7X-RAY DIFFRACTION7chain 'A' and (resid 438 through 478 )
8X-RAY DIFFRACTION8chain 'B' and (resid 212 through 345 )
9X-RAY DIFFRACTION9chain 'B' and (resid 346 through 437 )
10X-RAY DIFFRACTION10chain 'B' and (resid 438 through 477 )

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