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

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Basic information

Entry
Database: PDB / ID: 5iib
TitleCrystal structure of red abalone egg VERL repeat 3 in complex with sperm lysin at 1.64 A resolution (crystal form II)
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 / 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
sucrose / Egg-lysin / Vitelline envelope sperm lysin receptor
Similarity search - Component
Biological speciesHaliotis rufescens (red abalone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsRaj, I. / Sadat Al-Hosseini, H. / 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7516
Polymers30,7282
Non-polymers1,0234
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-9 kcal/mol
Surface area12500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.500, 64.500, 129.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-635-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Egg-lysin / Sperm-lysin


Mass: 16295.218 Da / Num. of mol.: 1
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: 14432.386 Da / Num. of mol.: 1
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

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Sugars , 2 types, 3 molecules

#3: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#5: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Source: (gene. exp.) Haliotis rufescens (red abalone) / 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

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Non-polymers , 2 types, 127 molecules

#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 1.6 M ammonium sulfate, 0.1 M citric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.64→32.25 Å / Num. obs: 39159 / % possible obs: 100 % / Redundancy: 5.4 % / Biso Wilson estimate: 34.67 Å2 / Rmerge(I) obs: 0.04848 / Net I/σ(I): 12.43
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 5.5 % / Rmerge(I) obs: 2.087 / Mean I/σ(I) obs: 0.85 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDS20141118data reduction
XDS20141118data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LIS

2lis


Resolution: 1.64→32.25 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.47
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1850 4.75 %Random selection
Rwork0.19 ---
obs0.191 38973 99.5 %-
Solvent computationShrinkage radii: 0.5 Å / VDW probe radii: 0.8 Å
Refinement stepCycle: LAST / Resolution: 1.64→32.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 66 126 2085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062020
X-RAY DIFFRACTIONf_angle_d0.9082746
X-RAY DIFFRACTIONf_dihedral_angle_d10.6321212
X-RAY DIFFRACTIONf_chiral_restr0.052305
X-RAY DIFFRACTIONf_plane_restr0.006336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.68430.4671370.41042792X-RAY DIFFRACTION99
1.6843-1.73390.37961390.36472792X-RAY DIFFRACTION99
1.7339-1.78990.3241400.32692855X-RAY DIFFRACTION100
1.7899-1.85380.33491410.29872788X-RAY DIFFRACTION100
1.8538-1.9280.30111420.26692840X-RAY DIFFRACTION100
1.928-2.01580.2351410.2282854X-RAY DIFFRACTION100
2.0158-2.1220.21041410.20342801X-RAY DIFFRACTION100
2.122-2.2550.2141420.19412857X-RAY DIFFRACTION100
2.255-2.4290.18951400.19082849X-RAY DIFFRACTION100
2.429-2.67330.22181450.19732880X-RAY DIFFRACTION100
2.6733-3.05990.24471440.20232873X-RAY DIFFRACTION99
3.0599-3.85420.2011430.17542915X-RAY DIFFRACTION100
3.8542-32.25620.15971550.1613027X-RAY DIFFRACTION99
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)
10.5410.7097-0.05590.9331-0.14921.03720.0463-0.1022-0.00430.2046-0.0831-0.03820.04590.0021-00.3949-0.03640.00680.33160.01470.356126.9412-4.46968.2782
20.54560.4089-0.07310.3716-0.26591.08820.03080.0112-0.0048-0.0681-0.0381-0.00980.06080.047700.4275-0.021-0.02420.27810.02130.351331.491-1.114-11.1172
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND NOT (RESNAME EPE)
2X-RAY DIFFRACTION2CHAIN B AND NOT (RESNAME SUC)

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