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- PDB-5mr2: Crystal structure of red abalone VERL repeat 2 with linker at 2.5... -

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Basic information

Entry
Database: PDB / ID: 5mr2
TitleCrystal structure of red abalone VERL repeat 2 with linker at 2.5 A resolution
ComponentsVitelline envelope sperm lysin receptor
KeywordsCELL ADHESION / FERTILIZATION / EGG-SPERM INTERACTION / GAMETE RECOGNITION / VITELLINE ENVELOPE / SPERM RECEPTOR
Function / homology
Function and homology information


vitelline envelope / sperm-egg recognition / extracellular region / plasma membrane
Similarity search - Function
Vitelline envelope, lysin receptor / Vitelline envelope receptor for lysin / Vitelline envelope sperm lysin receptor, C-terminal domain / ZP domain profile. / Zona pellucida domain
Similarity search - Domain/homology
Vitelline envelope sperm lysin receptor
Similarity search - Component
Biological speciesHaliotis rufescens (red abalone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSadat Al-Hosseini, H. / Raj, I. / Nishimura, K. / De Sanctis, D. / Jovine, L.
Funding support Sweden, 6items
OrganizationGrant numberCountry
Karolinska Institutet Sweden
Swedish Research Council2012-5093 Sweden
Goran Gustafsson Foundation for Research in Natural Sciences and Medicine Sweden
Sven and Ebba-Christina Hagberg foundation Sweden
European Molecular Biology Organization
European UnionERC 260759
Citation
Journal: Cell / Year: 2017
Title: Structural Basis of Egg Coat-Sperm Recognition at Fertilization.
Authors: Raj, I. / Sadat Al Hosseini, H. / Dioguardi, E. / Nishimura, K. / Han, L. / Villa, A. / de Sanctis, D. / Jovine, L.
#1: Journal: Mol. Biol. Evol. / Year: 2011
Title: The molecular basis of sex: linking yeast to human.
Authors: Swanson, W.J. / Aagaard, J.E. / Vacquier, V.D. / Monne, M. / Sadat Al Hosseini, H. / Jovine, L.
#2: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2006
Title: Rapidly evolving zona pellucida domain proteins are a major component of the vitelline envelope of abalone eggs.
Authors: Aagaard, J.E. / Yi, X. / MacCoss, M.J. / Swanson, W.J.
#3: Journal: Gene / Year: 2002
Title: Full-length sequence of VERL, the egg vitelline envelope receptor for abalone sperm lysin.
Authors: Galindo, B.E. / Moy, G.W. / Swanson, W.J. / Vacquier, V.D.
#4: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 1997
Title: The abalone egg vitelline envelope receptor for sperm lysin is a giant multivalent molecule.
Authors: Swanson, W.J. / Vacquier, V.D.
History
DepositionDec 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 17, 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 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vitelline envelope sperm lysin receptor
B: Vitelline envelope sperm lysin receptor
C: Vitelline envelope sperm lysin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9326
Polymers45,2683
Non-polymers6643
Water39622
1
C: Vitelline envelope sperm lysin receptor
hetero molecules

C: Vitelline envelope sperm lysin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6214
Polymers30,1792
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
2
A: Vitelline envelope sperm lysin receptor
B: Vitelline envelope sperm lysin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6214
Polymers30,1792
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-1 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.920, 79.190, 81.240
Angle α, β, γ (deg.)90.00, 102.62, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Vitelline envelope sperm lysin receptor


Mass: 15089.334 Da / Num. of mol.: 3 / Fragment: UNP residues 176-298 / Mutation: S293A, S296A, S297A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliotis rufescens (red abalone) / Gene: VERL / Plasmid: pHLsec / Cell line (production host): HEK-293S / Production host: Homo sapiens (human) / References: UniProt: Q8WR62
#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.: 3 / Mutation: S293A, S296A, S297A
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Source: (gene. exp.) Haliotis rufescens (red abalone) / Gene: VERL / Plasmid: pHLsec / Cell line (production host): HEK-293S / Production host: Homo sapiens (human)
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 0.2 M ammonium formate pH 6.6, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.5→47.01 Å / Num. obs: 15039 / % possible obs: 100 % / Redundancy: 4.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1382 / Net I/σ(I): 7.79
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 4.4 % / Rmerge(I) obs: 2.386 / Mean I/σ(I) obs: 0.62 / CC1/2: 0.222 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSMay 1, 2016 BUILT=20160617data reduction
XDSMay 1, 2016 BUILT=20160617data scaling
PHASER2.6.0phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IIA, 5IIB, 5IIC

5iia

5iib

5iic


Resolution: 2.5→47.006 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2802 1503 10.02 %
Rwork0.234 --
obs0.2386 14993 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→47.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 42 22 2572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082624
X-RAY DIFFRACTIONf_angle_d1.1323578
X-RAY DIFFRACTIONf_dihedral_angle_d13.732971
X-RAY DIFFRACTIONf_chiral_restr0.072407
X-RAY DIFFRACTIONf_plane_restr0.007446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58070.41321340.39591179X-RAY DIFFRACTION97
2.5807-2.67290.38971350.36421210X-RAY DIFFRACTION100
2.6729-2.780.37311370.34351230X-RAY DIFFRACTION100
2.78-2.90650.361360.31171232X-RAY DIFFRACTION100
2.9065-3.05970.3631340.30791203X-RAY DIFFRACTION100
3.0597-3.25130.34711380.27111238X-RAY DIFFRACTION100
3.2513-3.50230.28131360.24871229X-RAY DIFFRACTION100
3.5023-3.85460.25771370.23041231X-RAY DIFFRACTION100
3.8546-4.4120.25731380.19351240X-RAY DIFFRACTION100
4.412-5.55720.22071360.16951226X-RAY DIFFRACTION100
5.5572-47.01390.25831420.22121272X-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)
12.6503-0.0895-0.43894.28461.28713.09320.02990.23820.037-0.2072-0.13910.2613-0.3496-0.1949-00.5851-0.02090.02570.6345-0.00490.634311.56667.9431-3.9007
22.8110.1029-0.70595.50070.68115.9477-0.17680.2926-0.0486-0.2630.2008-0.2194-0.2820.165700.4731-0.0817-0.01210.6208-0.06660.700621.7244-7.532-14.7795
31.2283-0.37480.20972.8244-0.56415.96750.1902-0.0016-0.1275-0.12360.0302-0.0488-0.0054-0.1717-00.6108-0.0263-0.03860.58230.02510.650220.237415.849430.818
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and not resname HOH
2X-RAY DIFFRACTION2chain B and not resname HOH
3X-RAY DIFFRACTION3chain C and not resname HOH

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