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- PDB-5ii4: Crystal structure of red abalone VERL repeat 1 with linker at 2.0... -

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Entry
Database: PDB / ID: 5ii4
TitleCrystal structure of red abalone VERL repeat 1 with linker at 2.0 A resolution
ComponentsMaltose-binding periplasmic protein,Vitelline 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 / carbohydrate transmembrane transporter activity / outer membrane-bounded periplasmic space / extracellular region / plasma membrane
Similarity search - Function
Vitelline envelope, lysin receptor / Vitelline envelope receptor for lysin / ZP domain profile. / Zona pellucida domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / TRIETHYLENE GLYCOL / Maltose/maltodextrin-binding periplasmic protein / Vitelline envelope sperm lysin receptor
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Haliotis rufescens (red abalone)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSadat Al-Hosseini, H. / Raj, I. / Nishimura, K. / 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
DepositionMar 1, 2016Deposition site: RCSB / 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_conn_type / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _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.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

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Vitelline envelope sperm lysin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6987
Polymers56,6051
Non-polymers1,0936
Water2,180121
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint17 kcal/mol
Surface area20610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.120, 107.120, 195.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Maltose-binding periplasmic protein,Vitelline envelope sperm lysin receptor / MBP / MMBP / Maltodextrin-binding protein


Mass: 56604.797 Da / Num. of mol.: 1
Mutation: N4115Q, N4122T, N4142Y, N4171Q,N4115Q, N4122T, N4142Y, N4171Q,N4115Q, N4122T, N4142Y, N4171Q,N4115Q, N4122T, N4142Y, N4171Q
Source method: isolated from a genetically manipulated source
Details: THIS PROTEIN IS A CHIMERA. RESIDUES 3668-4034 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 27-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS I3669T, ...Details: THIS PROTEIN IS A CHIMERA. RESIDUES 3668-4034 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 27-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS I3669T, D3749A, K3750A, E3839A, N3840A, A3882H, K3886H, K3906A, A3979V, I3984V, E4026A, E4029A, D4030A AND R4034N (CORRESPONDING TO I28T, D108A, K109A, E198A, N199A, A241H, K245H, K265A, A338V, I343V, E385A, E388A, D389A AND R393N IN P0AEX9). RESIDUES 4038-4175 ARE FROM RED ABALONE VITELLINE ENVELOPE SPERM LYSIN RECEPTOR AND CORRESPOND TO RESIDUES 38-175 OF SWISS-PROT DATABASE ENTRY Q8WR62 AND CONTAIN MUTATIONS N4115Q, N4122T, N4142Y AND N4171Q (CORRESPONDING TO N115Q, N122T, N142Y AND N171Q).
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Haliotis rufescens (red abalone)
Gene: malE, Z5632, ECs5017, VERL / Plasmid: pHLsec / Cell line (production host): HEK-293T / Production host: Homo sapiens (human) / References: UniProt: P0AEY0, UniProt: Q8WR62
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 5 / Mutation: N4115Q, N4122T, N4142Y, N4171Q
Source method: isolated from a genetically manipulated source
Formula: C6H14O4
Details: THIS PROTEIN IS A CHIMERA. RESIDUES 3668-4034 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 27-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS I3669T, ...Details: THIS PROTEIN IS A CHIMERA. RESIDUES 3668-4034 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 27-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS I3669T, D3749A, K3750A, E3839A, N3840A, A3882H, K3886H, K3906A, A3979V, I3984V, E4026A, E4029A, D4030A AND R4034N (CORRESPONDING TO I28T, D108A, K109A, E198A, N199A, A241H, K245H, K265A, A338V, I343V, E385A, E388A, D389A AND R393N IN P0AEX9). RESIDUES 4038-4175 ARE FROM RED ABALONE VITELLINE ENVELOPE SPERM LYSIN RECEPTOR AND CORRESPOND TO RESIDUES 38-175 OF SWISS-PROT DATABASE ENTRY Q8WR62 AND CONTAIN MUTATIONS N4115Q, N4122T, N4142Y AND N4171Q (CORRESPONDING TO N115Q, N122T, N142Y AND N171Q).
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: malE / Plasmid: pHLsec / Cell line (production host): HEK-293T / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 40% PEG 600, 0.1M CHES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→46.991 Å / Num. obs: 44601 / % possible obs: 98 % / Redundancy: 4.9 % / Biso Wilson estimate: 36.16 Å2 / Rmerge(I) obs: 0.1027 / Net I/σ(I): 8.84
Reflection shellResolution: 2→2.072 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.446 / Mean I/σ(I) obs: 1.01 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIXdev-1894_1692refinement
XDS20141103data reduction
XDS20141103data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SET, 3SEX and 4WRN

3set

3sex

4wrn


Resolution: 2→46.991 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.97
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 2287 5.13 %Random selection
Rwork0.2179 ---
obs0.2193 44558 97.76 %-
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Refinement stepCycle: LAST / Resolution: 2→46.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3759 0 0 121 3880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063850
X-RAY DIFFRACTIONf_angle_d0.9075222
X-RAY DIFFRACTIONf_dihedral_angle_d11.1351401
X-RAY DIFFRACTIONf_chiral_restr0.038577
X-RAY DIFFRACTIONf_plane_restr0.005662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.04360.41061460.39832571X-RAY DIFFRACTION97
2.0436-2.09110.37631350.38122616X-RAY DIFFRACTION99
2.0911-2.14340.3351440.34722630X-RAY DIFFRACTION99
2.1434-2.20130.34781360.31412618X-RAY DIFFRACTION99
2.2013-2.26610.32611430.32182625X-RAY DIFFRACTION99
2.2661-2.33930.31021390.27352616X-RAY DIFFRACTION99
2.3393-2.42290.27291410.25592628X-RAY DIFFRACTION99
2.4229-2.51990.2511420.24872630X-RAY DIFFRACTION99
2.5199-2.63450.24831400.23132632X-RAY DIFFRACTION99
2.6345-2.77340.23941390.21812635X-RAY DIFFRACTION98
2.7734-2.94720.22881560.21682643X-RAY DIFFRACTION98
2.9472-3.17470.23581330.22232643X-RAY DIFFRACTION98
3.1747-3.4940.26311480.19892664X-RAY DIFFRACTION98
3.494-3.99940.23871500.18292646X-RAY DIFFRACTION97
3.9994-5.03790.19391350.16162672X-RAY DIFFRACTION96
5.0379-47.00350.2181600.19692802X-RAY DIFFRACTION94
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)
11.10430.2681-0.41320.7239-0.63043.55070.01310.08890.12880.01490.04090.1029-0.3148-0.27810.0040.3134-0.05120.01040.3727-0.02260.398369.937959.331510.2657
21.8226-1.0584-0.19880.70760.40131.4943-0.0546-0.2156-0.2447-0.19420.16010.00390.11770.5526-00.4263-0.00230.02970.68160.01190.476195.292244.7573-6.1313
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resi 39:407 or resi 900)
2X-RAY DIFFRACTION2chain A and resi 408:515

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