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- PDB-7kbu: Structure of Hevin FS-EC -

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Basic information

Entry
Database: PDB / ID: 7kbu
TitleStructure of Hevin FS-EC
ComponentsProliferation-inducing protein 33
KeywordsCELL ADHESION / hevin / SPARC / neurexins / neuroligins / MDGAs / synaptic organizer / adhesion molecule
Function / homology
Function and homology information


protein metabolic process => GO:0019538 / anatomical structure development / synaptic membrane adhesion / extracellular matrix binding / collagen binding / post-translational protein modification / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / collagen-containing extracellular matrix / endoplasmic reticulum lumen ...protein metabolic process => GO:0019538 / anatomical structure development / synaptic membrane adhesion / extracellular matrix binding / collagen binding / post-translational protein modification / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / collagen-containing extracellular matrix / endoplasmic reticulum lumen / glutamatergic synapse / calcium ion binding / signal transduction / extracellular space / extracellular region
Similarity search - Function
SPARC-like protein 1 / Osteonectin-like, conserved site / SPARC/Testican, calcium-binding domain / Osteonectin domain signature 1. / Osteonectin domain signature 2. / Secreted protein acidic and rich in cysteine Ca binding region / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like ...SPARC-like protein 1 / Osteonectin-like, conserved site / SPARC/Testican, calcium-binding domain / Osteonectin domain signature 1. / Osteonectin domain signature 2. / Secreted protein acidic and rich in cysteine Ca binding region / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Kazal-type serine protease inhibitor domain / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
FORMIC ACID / SPARC-like protein 1 / SPARC-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.27 Å
AuthorsMachius, M. / Fan, S. / Rudenko, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01MH077303 United States
CitationJournal: Structure / Year: 2021
Title: Interplay between hevin, SPARC, and MDGAs: Modulators of neurexin-neuroligin transsynaptic bridges.
Authors: Fan, S. / Gangwar, S.P. / Machius, M. / Rudenko, G.
History
DepositionOct 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proliferation-inducing protein 33
B: Proliferation-inducing protein 33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,54619
Polymers57,1072
Non-polymers1,43817
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, Analytical ultracentrifugation, size-exclusion chromatography, cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8000 Å2
ΔGint-140 kcal/mol
Surface area22090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.657, 132.289, 149.225
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Proliferation-inducing protein 33 / SPARC-like 1 (Hevin)


Mass: 28553.697 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPARCL1, PIG33 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N4S1, UniProt: Q14515*PLUS
#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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 176 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.49 Å3/Da / Density % sol: 50.63 % / Description: Crystals were diamond-shaped with clean edges
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3 microliters of protein solution (12 mg/ml in 10 mM Tris, pH 7.5, 2 mM CaCl2) were mixed with 3 microliters of crystallization solution (14% (w/v) Peg 4000, 0.15 M sodium acetate, 0.1 M ...Details: 3 microliters of protein solution (12 mg/ml in 10 mM Tris, pH 7.5, 2 mM CaCl2) were mixed with 3 microliters of crystallization solution (14% (w/v) Peg 4000, 0.15 M sodium acetate, 0.1 M HEPES, pH 7.5) and equilibrated against crystallization solution. Diamond-shaped crystals grew within ~10 days and were up to 200 micrometers in length.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.27→33 Å / Num. obs: 26686 / % possible obs: 99.8 % / Redundancy: 12.7 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.018 / Rrim(I) all: 1.012 / Χ2: 0.061 / Net I/σ(I): 36.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.27-2.317.91.2661.913090.6940.9050.4491.3450.82999.1
2.31-2.3591.0912.613020.7640.9310.3611.1510.83699.3
2.35-2.410.20.9433.213320.8450.9570.2970.990.85299.9
2.4-2.4510.90.795412830.9070.9750.2440.8320.848100
2.45-2.5110.635513410.9250.980.1970.6660.87100
2.5-2.5612.30.4737.212900.9650.9910.1380.4930.912100
2.56-2.6212.10.3838.813390.9760.9940.1140.40.933100
2.62-2.6913.20.311.513120.9820.9950.0850.3120.956100
2.69-2.7713.10.24913.613290.9890.9970.0710.260.976100
2.77-2.8612.90.18818.213400.990.9980.0540.1961.054100
2.86-2.9612.50.14921.213080.9940.9980.0440.1551.09100
2.96-3.0811.90.11725.313240.9930.0350.1221.129100
3.08-3.2212.20.09431.713440.9960.9990.0280.0981.188100
3.22-3.3913.20.07739.313310.9980.9990.0220.081.254100
3.39-3.6130.06543.513390.9980.9990.0190.0671.257100
3.6-3.8812.50.05544.613480.99910.0160.0581.196100
3.88-4.2712.40.0484513410.99910.0140.051.07399.9
4.27-4.8913.30.04448.213570.99910.0130.0461.035100
4.89-6.1612.20.04445.913710.99910.0130.0450.94100
6.16-3311.60.0440.214460.99810.0120.0420.78498.6

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassification
PHENIX(1.19rc7_4070: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
AutoSolphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.27→33 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2378 1298 5 %
Rwork0.1865 --
obs0.1891 25958 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3357 0 79 161 3597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083547
X-RAY DIFFRACTIONf_angle_d0.9024794
X-RAY DIFFRACTIONf_dihedral_angle_d5.102471
X-RAY DIFFRACTIONf_chiral_restr0.046517
X-RAY DIFFRACTIONf_plane_restr0.007617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.360.29721100.22452098X-RAY DIFFRACTION76
2.36-2.470.25891440.19442727X-RAY DIFFRACTION98
2.47-2.60.23941460.19012775X-RAY DIFFRACTION100
2.6-2.760.25821470.18492796X-RAY DIFFRACTION100
2.76-2.980.28421470.19512804X-RAY DIFFRACTION100
2.98-3.280.251480.19562797X-RAY DIFFRACTION100
3.28-3.750.23231490.16952834X-RAY DIFFRACTION100
3.75-4.720.18761510.15782873X-RAY DIFFRACTION100
4.72-330.24291560.20992956X-RAY DIFFRACTION100
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)
10.7390.03320.00853.3376-1.07681.640.0199-0.07180.2031-0.46510.0414-0.01850.08580.0888-0.00010.1855-0.01750.02910.2495-0.06910.180742.731286.773447.7381
22.0962-0.9592-0.06181.10560.03753.00990.093-0.3021-0.1059-0.08170.16270.3733-0.035-0.37890.08610.1289-0.0198-0.02470.24340.0650.314326.424375.521459.4143
31.0022-0.15051.03632.1207-0.39111.58190.21390.0277-0.59360.0065-0.21190.58840.99780.3516-0.00920.73340.0660.03860.1815-0.01980.380239.921842.699351.4748
41.28360.16610.86992.58460.1943.06640.1028-0.0298-0.05540.00570.0071-0.4340.28850.71050.04770.09560.05120.02610.3382-0.01390.160951.069669.341761.0882
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 431 through 542 )
2X-RAY DIFFRACTION2chain 'A' and (resid 543 through 663 )
3X-RAY DIFFRACTION3chain 'B' and (resid 438 through 506 )
4X-RAY DIFFRACTION4chain 'B' and (resid 507 through 666 )

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