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- PDB-5iia: Crystal structure of red abalone egg VERL repeat 3 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5iia
TitleCrystal structure of red abalone egg VERL repeat 3 in complex with sperm lysin at 1.7 A resolution (crystal form I)
Components
  • Egg-lysin
  • Vitelline envelope sperm lysin receptor
KeywordsCELL ADHESION / FERTILIZATION / EGG-SPERM INTERACTION / GAMETE RECOGNITION / SPERM RECEPTOR / EGG COAT / VITELLINE ENVELOPE / ZP DOMAIN / ZP-N DOMAIN / SPERM ACROSOME / EGG COAT PENETRATION
Function / homology
Function and homology information


vitelline envelope / acrosomal lumen / sperm-egg recognition / single fertilization / extracellular region / plasma membrane
Similarity search - Function
Vitelline envelope, lysin receptor / Vitelline envelope receptor for lysin / Vitelline envelope sperm lysin receptor, C-terminal domain / Fertilization protein / Egg lysin (Sperm-lysin) / Egg-lysin superfamily / Egg lysin (Sperm-lysin) / ZP domain profile. / Zona pellucida domain / Lysin ...Vitelline envelope, lysin receptor / Vitelline envelope receptor for lysin / Vitelline envelope sperm lysin receptor, C-terminal domain / Fertilization protein / Egg lysin (Sperm-lysin) / Egg-lysin superfamily / Egg lysin (Sperm-lysin) / ZP domain profile. / Zona pellucida domain / Lysin / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Egg-lysin / Vitelline envelope sperm lysin receptor
Similarity search - Component
Biological speciesHaliotis rufescens (red abalone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: Acta Crystallogr. D Biol. Crystallogr. / Year: 2000
Title: 1.35 and 2.07 A resolution structures of the red abalone sperm lysin monomer and dimer reveal features involved in receptor binding.
Authors: Kresge, N. / Vacquier, V.D. / Stout, C.D.
#5: 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.
#6: Journal: J. Cell Biol. / Year: 1995
Title: Crystal structure and subunit dynamics of the abalone sperm lysin dimer: egg envelopes dissociate dimers, the monomer is the active species.
Authors: Shaw, A. / Fortes, P.A. / Stout, C.D. / Vacquier, V.D.
#7: Journal: Science / Year: 1993
Title: The crystal structure of lysin, a fertilization protein.
Authors: Shaw, A. / McRee, D.E. / Vacquier, V.D. / Stout, C.D.
History
DepositionMar 1, 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 1.3Nov 29, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.4Jul 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 1.5Jan 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 1.6Nov 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: Egg-lysin
B: Vitelline envelope sperm lysin receptor
C: Egg-lysin
D: Vitelline envelope sperm lysin receptor
E: Egg-lysin
F: Vitelline envelope sperm lysin receptor
G: Egg-lysin
H: Vitelline envelope sperm lysin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,18916
Polymers123,4198
Non-polymers1,7708
Water10,395577
1
A: Egg-lysin
B: Vitelline envelope sperm lysin receptor
C: Egg-lysin
D: Vitelline envelope sperm lysin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5948
Polymers61,7094
Non-polymers8854
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-35 kcal/mol
Surface area23190 Å2
MethodPISA
2
E: Egg-lysin
F: Vitelline envelope sperm lysin receptor
G: Egg-lysin
H: Vitelline envelope sperm lysin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5948
Polymers61,7094
Non-polymers8854
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-35 kcal/mol
Surface area23270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.490, 60.330, 89.170
Angle α, β, γ (deg.)105.04, 89.02, 113.28
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Egg-lysin / Sperm-lysin


Mass: 16295.218 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliotis rufescens (red abalone) / Cell line (production host): HEK-293S / Production host: Homo sapiens (human) / References: UniProt: P04552
#2: Protein
Vitelline envelope sperm lysin receptor


Mass: 14559.529 Da / Num. of mol.: 4 / Fragment: UNP residues 340-453
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliotis rufescens (red abalone) / Gene: VERL / Cell line (production host): HEK-293S / Production host: Homo sapiens (human) / References: UniProt: Q8WR62
#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.: 8
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 577 / 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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 20% PEG 3350, 0.2 M di-ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 1.7→48.655 Å / Num. obs: 122478 / % possible obs: 97 % / Redundancy: 3.5 % / Biso Wilson estimate: 35.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04912 / Net I/σ(I): 9.63
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.765 / Mean I/σ(I) obs: 0.79 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(dev_2689: ???)refinement
XDS20141118data reduction
XDS20141118data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LIS

2lis


Resolution: 1.7→48.655 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2035 3799 3.19 %Random selection
Rwork0.1774 ---
obs0.1783 119230 97.35 %-
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→48.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7535 0 112 577 8224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087887
X-RAY DIFFRACTIONf_angle_d1.12810698
X-RAY DIFFRACTIONf_dihedral_angle_d12.2722988
X-RAY DIFFRACTIONf_chiral_restr0.0521176
X-RAY DIFFRACTIONf_plane_restr0.0071332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72160.39611360.41084252X-RAY DIFFRACTION96
1.7216-1.74420.34481390.38754227X-RAY DIFFRACTION96
1.7442-1.76810.41361420.37424205X-RAY DIFFRACTION97
1.7681-1.79340.40331400.36234228X-RAY DIFFRACTION97
1.7934-1.82010.3431450.34694250X-RAY DIFFRACTION97
1.8201-1.84860.35611410.32834240X-RAY DIFFRACTION97
1.8486-1.87890.34861380.30744246X-RAY DIFFRACTION97
1.8789-1.91130.31171360.29034273X-RAY DIFFRACTION97
1.9113-1.9460.33331430.27924252X-RAY DIFFRACTION97
1.946-1.98350.26841390.26454158X-RAY DIFFRACTION96
1.9835-2.0240.28841430.24434239X-RAY DIFFRACTION95
2.024-2.0680.2381400.22184277X-RAY DIFFRACTION97
2.068-2.11610.22911340.2024191X-RAY DIFFRACTION97
2.1161-2.1690.22131490.18974325X-RAY DIFFRACTION98
2.169-2.22760.21761290.17574302X-RAY DIFFRACTION97
2.2276-2.29320.19911420.17584245X-RAY DIFFRACTION98
2.2932-2.36720.18811430.17134303X-RAY DIFFRACTION98
2.3672-2.45180.18431370.17164294X-RAY DIFFRACTION98
2.4518-2.550.21671420.18824350X-RAY DIFFRACTION98
2.55-2.6660.20151500.18224264X-RAY DIFFRACTION97
2.666-2.80660.23731370.18364295X-RAY DIFFRACTION99
2.8066-2.98240.22911470.18014376X-RAY DIFFRACTION99
2.9824-3.21260.22391430.17584319X-RAY DIFFRACTION99
3.2126-3.53580.19521370.16374345X-RAY DIFFRACTION99
3.5358-4.04720.19171400.14954327X-RAY DIFFRACTION98
4.0472-5.09820.13451470.12024345X-RAY DIFFRACTION99
5.0982-48.67530.16881400.16664303X-RAY DIFFRACTION98
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)
12.58030.21330.86711.6060.4321.52480.01480.040.11310.0008-0.0194-0.0579-0.0279-0.0316-00.31080.00950.00430.3234-0.00070.303619.025826.525336.2997
22.9008-1.0471-0.98871.59520.34122.21940.05930.14050.1617-0.0331-0.0265-0.0892-0.06580.01040.00070.3498-0.00660.00490.38590.01120.355835.712819.646327.765
31.99070.30740.13122.02641.05212.5396-0.08640.1125-0.07860.0583-0.00660.10040.1266-0.080800.3336-0.00290.02670.3249-0.00690.305859.83180.18560.5327
42.8408-0.703-0.82361.62171.05182.9609-0.13820.0822-0.06760.1302-0.02610.11720.2089-0.1016-0.00230.3611-0.02970.03490.42290.00160.400450.130210.342715.4727
52.2599-0.27181.00072.0013-0.52432.54980.0672-0.09950.00050.008-0.1229-0.13640.02470.1474-00.3997-0.01170.01250.35620.02940.3426-4.99166.106980.7613
61.87970.1844-0.80122.7065-0.9832.91940.07080.06160.1053-0.1196-0.0757-0.09780.04330.072-0.00020.45520.00240.04780.38870.02150.372-5.925519.837565.9527
71.97790.38750.483.52640.17321.5156-0.0201-0.042-0.00150.30520.07360.061-0.0614-0.0428-00.37670.0210.0130.32680.02950.34244.055752.956344.6587
82.22540.3295-0.71322.7155-1.2272.09540.03490.00960.09390.33220.10510.1804-0.0169-0.07720.00420.46330.0360.0580.38020.0430.3663-2.353435.853653.2476
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
4X-RAY DIFFRACTION4chain D and not resname HOH
5X-RAY DIFFRACTION5chain E and not resname HOH
6X-RAY DIFFRACTION6chain F and not resname HOH
7X-RAY DIFFRACTION7chain G and not resname HOH
8X-RAY DIFFRACTION8chain H and not resname HOH

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