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- PDB-5mr3: Crystal structure of red abalone egg VERL repeat 2 with linker in... -

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Basic information

Entry
Database: PDB / ID: 5mr3
TitleCrystal structure of red abalone egg VERL repeat 2 with linker in complex with sperm lysin at 1.8 A resolution
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 / SPERM 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
TRIETHYLENE GLYCOL / Egg-lysin / Vitelline envelope sperm lysin receptor
Similarity search - Component
Biological speciesHaliotis rufescens (red abalone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNishimura, K. / Raj, I. / Sadat Al-Hosseini, H. / 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
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 2.0Jul 26, 2017Group: Advisory / Database references ...Advisory / Database references / Polymer sequence / Source and taxonomy / Structure summary
Category: entity / entity_poly ...entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq
Item: _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code ..._entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 2.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Nov 22, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 2.3Jul 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 2.4Jan 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

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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)127,89928
Polymers125,5388
Non-polymers2,36120
Water10,070559
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)63,98415
Polymers62,7694
Non-polymers1,21511
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9320 Å2
ΔGint-51 kcal/mol
Surface area24070 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)63,91613
Polymers62,7694
Non-polymers1,1479
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8560 Å2
ΔGint-40 kcal/mol
Surface area24970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.870, 87.860, 92.550
Angle α, β, γ (deg.)90.00, 100.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#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) / Production host: Homo sapiens (human) / References: UniProt: P04552
#2: Protein
Vitelline envelope sperm lysin receptor


Mass: 15089.334 Da / Num. of mol.: 4 / 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

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Sugars , 1 types, 4 molecules

#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.: 4 / 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

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Non-polymers , 4 types, 575 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 5% (w/v) PEG 8000, 20% (v/v) PEG 300, 10% (v/v) Glycerol, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 1.8→45.322 Å / Num. obs: 109995 / % possible obs: 99.5 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.05377 / Net I/σ(I): 11.53
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.494 / Mean I/σ(I) obs: 0.97 / CC1/2: 0.307 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSMay 1, 2016 BUILT=20160617data reduction
XDSMay 1, 2016 BUILT=20160617data scaling
PHASER2.7.12phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 5II8, 5II9, D_1200000737

5ii8

5ii9


Resolution: 1.8→45.322 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.68
RfactorNum. reflection% reflection
Rfree0.227 5503 5 %
Rwork0.2008 --
obs0.2021 109973 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→45.322 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7878 0 94 559 8531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058193
X-RAY DIFFRACTIONf_angle_d0.79311079
X-RAY DIFFRACTIONf_dihedral_angle_d13.7933106
X-RAY DIFFRACTIONf_chiral_restr0.051188
X-RAY DIFFRACTIONf_plane_restr0.0071375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82040.4331840.4123472X-RAY DIFFRACTION99
1.8204-1.84180.44861820.39793491X-RAY DIFFRACTION100
1.8418-1.86430.4021810.37263452X-RAY DIFFRACTION100
1.8643-1.88790.39761840.36053480X-RAY DIFFRACTION100
1.8879-1.91270.37251830.35553458X-RAY DIFFRACTION100
1.9127-1.93890.37661830.34063474X-RAY DIFFRACTION100
1.9389-1.96660.31081820.31873477X-RAY DIFFRACTION100
1.9666-1.9960.35291850.30763512X-RAY DIFFRACTION100
1.996-2.02720.33331810.30043435X-RAY DIFFRACTION100
2.0272-2.06040.30071830.28043481X-RAY DIFFRACTION100
2.0604-2.09590.28511830.2673471X-RAY DIFFRACTION100
2.0959-2.13410.30091820.2563459X-RAY DIFFRACTION100
2.1341-2.17510.25821850.24953490X-RAY DIFFRACTION100
2.1751-2.21950.27191820.2393460X-RAY DIFFRACTION100
2.2195-2.26780.27371800.23783440X-RAY DIFFRACTION99
2.2678-2.32050.26521870.22653530X-RAY DIFFRACTION99
2.3205-2.37850.24631830.22133451X-RAY DIFFRACTION100
2.3785-2.44280.27971800.21593452X-RAY DIFFRACTION99
2.4428-2.51470.25771890.22493492X-RAY DIFFRACTION100
2.5147-2.59590.23631780.20953460X-RAY DIFFRACTION100
2.5959-2.68870.20631820.20953494X-RAY DIFFRACTION100
2.6887-2.79630.2431840.2093481X-RAY DIFFRACTION100
2.7963-2.92350.23071850.20523508X-RAY DIFFRACTION100
2.9235-3.07760.20441820.19933479X-RAY DIFFRACTION100
3.0776-3.27040.21681880.19523499X-RAY DIFFRACTION100
3.2704-3.52280.19981810.1763500X-RAY DIFFRACTION100
3.5228-3.87720.1951840.16033494X-RAY DIFFRACTION99
3.8772-4.43780.17511850.1473483X-RAY DIFFRACTION99
4.4378-5.58950.16421840.14113521X-RAY DIFFRACTION100
5.5895-45.33660.21871910.19283574X-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)
13.8271-0.86480.85612.8254-0.13613.1913-0.1134-0.47620.15680.1817-0.19170.0392-0.4217-0.1027-0.04690.3669-0.0302-0.02320.3409-0.06510.283322.943837.014842.6791
22.82420.0460.95041.57350.77471.9736-0.0048-0.29820.1604-0.0131-0.08310.1551-0.0907-0.2235-0.00580.32050.01090.01860.3036-0.03680.368211.101929.976126.1517
32.5828-0.43971.8523.4935-0.03522.99570.0562-0.1868-0.0246-0.0570.01890.15110.264-0.52190.01010.3737-0.0181-0.0420.4048-0.09650.3743-7.36765.26320.4156
41.70610.31160.03832.66811.79883.5601-0.0268-0.154-0.1254-0.1809-0.31570.4338-0.0569-0.3811-0.01820.29370.045-0.04740.3084-0.08160.41410.026719.275513.1475
52.05090.4-0.3911.7906-0.42993.52290.04980.0861-0.2144-0.11330.1078-0.0490.38790.34030.00170.38280.0502-0.01980.3119-0.06360.338821.8391-0.261114.0101
62.88550.76610.13892.86990.34282.36070.01040.2442-0.2339-0.09110.0119-0.36650.07360.40180.00970.25810.02740.03430.4491-0.05630.314533.376515.335615.8963
71.22990.2453-0.76711.28680.95984.19210.054-0.01320.1276-0.08340.019-0.1809-0.57310.29790.00110.4532-0.07020.04430.4105-0.00560.430952.186247.270733.8173
83.836-0.3449-0.51953.41480.76983.00060.01760.24710.0544-0.08880.0915-0.0798-0.2930.1153-0.00020.3011-0.07170.04240.459-0.01340.306244.207132.6123.6994
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (not (resname GOL or resname PGE))
2X-RAY DIFFRACTION2chain B and (not (resname GOL or resname PGE))
3X-RAY DIFFRACTION3chain C and (not (resname GOL or resname PGE))
4X-RAY DIFFRACTION4chain D and (not (resname GOL or resname PGE))
5X-RAY DIFFRACTION5chain E and (not (resname GOL or resname PGE))
6X-RAY DIFFRACTION6chain F and (not (resname GOL or resname PGE))
7X-RAY DIFFRACTION7chain G and (not (resname GOL or resname PGE))
8X-RAY DIFFRACTION8chain H and (not (resname GOL or resname PGE))

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