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- PDB-5iic: Crystal structure of red abalone VERL repeat 3 at 2.9 A resolution -

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Entry
Database: PDB / ID: 5iic
TitleCrystal structure of red abalone VERL repeat 3 at 2.9 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 / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing ...vitelline envelope / sperm-egg recognition / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / extracellular region / membrane / 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 / 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 ...Vitelline envelope, lysin receptor / Vitelline envelope receptor for lysin / Vitelline envelope sperm lysin receptor, C-terminal domain / 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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Vitelline envelope sperm lysin receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Haliotis rufescens (red abalone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSadat Al-Hosseini, H. / Raj, I. / Nishimura, K. / Jovine, L.
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 1.2Nov 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 / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / entity_src_gen / 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_asym / 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.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_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.details / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_asym.entity_id
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
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: Maltose-binding periplasmic protein,Vitelline envelope sperm lysin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,6718
Polymers109,1012
Non-polymers1,5696
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-4 kcal/mol
Surface area37550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.330, 81.640, 111.630
Angle α, β, γ (deg.)90.00, 99.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 54550.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THIS PROTEIN IS A CHIMERA. RESIDUES 3969-4336 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 26-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS A3969T, ...Details: THIS PROTEIN IS A CHIMERA. RESIDUES 3969-4336 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 26-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS A3969T, D4051A, K4052A, E4141A, N4142A, A4184H, K4188H, K4208A, A4281V, I4286V, E4328A, E4331A, D4332A AND R4336N (CORRESPONDING TO A26T, D108A, K109A, E198A, N199A, A241H, K245H, K265A, A338V, I343V, E385A, E388A, D389A AND R393N IN P0AEX9). RESIDUES 4340-4453 ARE FROM RED ABALONE VITELLINE ENVELOPE SPERM LYSIN RECEPTOR AND CORRESPOND TO RESIDUES 340-453 OF SWISS-PROT DATABASE ENTRY Q8WR62.
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Haliotis rufescens (red abalone)
Strain: K12 / Gene: malE, b4034, JW3994, VERL / Plasmid: pHLsec / Cell line (production host): HEK-293S / Production host: Homo sapiens (human) / References: UniProt: P0AEX9, 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.: 2
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: 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.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
Details: THIS PROTEIN IS A CHIMERA. RESIDUES 3969-4336 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 26-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS A3969T, ...Details: THIS PROTEIN IS A CHIMERA. RESIDUES 3969-4336 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 26-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS A3969T, D4051A, K4052A, E4141A, N4142A, A4184H, K4188H, K4208A, A4281V, I4286V, E4328A, E4331A, D4332A AND R4336N (CORRESPONDING TO A26T, D108A, K109A, E198A, N199A, A241H, K245H, K265A, A338V, I343V, E385A, E388A, D389A AND R393N IN P0AEX9). RESIDUES 4340-4453 ARE FROM RED ABALONE VITELLINE ENVELOPE SPERM LYSIN RECEPTOR AND CORRESPOND TO RESIDUES 340-453 OF SWISS-PROT DATABASE ENTRY Q8WR62.
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: malE / 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
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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG 4000, 20% isopropanol, 0.1M tri-sodium citrate

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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: Jan 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.9→47.805 Å / Num. obs: 22737 / % possible obs: 98 % / Redundancy: 4 % / Biso Wilson estimate: 68.84 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1734 / Net I/σ(I): 7.32
Reflection shellResolution: 2.9→3.004 Å / Redundancy: 4 % / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 1.2 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDS20141118data reduction
XDS20141118data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SET, 3SEX and 4WRN

3set

3sex

4wrn


Resolution: 2.9→47.017 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.08
RfactorNum. reflection% reflectionSelection details
Rfree0.3096 1189 5.24 %Random selection
Rwork0.2514 ---
obs0.2545 22700 98.24 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 2.9→47.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7360 0 0 0 7360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037549
X-RAY DIFFRACTIONf_angle_d0.54810284
X-RAY DIFFRACTIONf_dihedral_angle_d9.934485
X-RAY DIFFRACTIONf_chiral_restr0.0421157
X-RAY DIFFRACTIONf_plane_restr0.0041309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.0320.42051420.40812656X-RAY DIFFRACTION97
3.032-3.19180.3971400.36832675X-RAY DIFFRACTION99
3.1918-3.39170.3971570.32932683X-RAY DIFFRACTION98
3.3917-3.65350.33521340.29252697X-RAY DIFFRACTION98
3.6535-4.0210.34341530.25762660X-RAY DIFFRACTION98
4.021-4.60240.27491590.22492706X-RAY DIFFRACTION99
4.6024-5.79680.25441520.20372701X-RAY DIFFRACTION99
5.7968-47.02340.28011520.20352733X-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)
10.9429-0.2260.43720.5988-0.57992.22310.0424-0.142-0.0005-0.078-0.19760.0985-0.1034-0.086200.37120.00060.00710.5237-0.09080.468110.9423-0.189848.1651
20.90430.53820.03540.5936-0.58720.7526-0.2001-0.16170.0401-0.23270.0985-0.0380.2720.077300.84680.08460.00260.77280.01510.588229.9775-17.383140.5424
31.23910.0141-0.5561.96710.57451.045-0.0856-0.0286-0.1599-0.2038-0.03410.2051-0.37-0.0063-0.00040.72140.0778-0.05120.3513-0.0230.524215.228-18.5133.4697
40.66360.4061-0.23580.41880.0640.5825-0.0890.02730.05110.21330.037-0.2566-0.1411-0.1223-00.6658-0.02020.02180.61650.00930.558333.9331.335518.4146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resi 3969:4339 or resi 4900)
2X-RAY DIFFRACTION2chain A and (resi 4340:4448 or resi 4910 or resi 4920)
3X-RAY DIFFRACTION3chain B and (resi 3974:4339 or resi 4900)
4X-RAY DIFFRACTION4chain B and (resi 4340:4448 or resi 4910 or resi 4920)

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