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- PDB-3d4c: ZP-N domain of mammalian sperm receptor ZP3 (crystal form I) -

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Entry
Database: PDB / ID: 3d4c
TitleZP-N domain of mammalian sperm receptor ZP3 (crystal form I)
ComponentsMaltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
KeywordsCELL ADHESION / fertilization / oocyte / egg coat / zona pellucida / vitelline envelope / zp domain / egg-sperm interaction / species-specific gamete recognition / speciation / biodiversity / infertility / extracellular matrix / immunoglobulin-like fold / glycoprotein / receptor / secreted / transmembrane
Function / homology
Function and homology information


positive regulation of type IV hypersensitivity / positive regulation of acrosomal vesicle exocytosis / positive regulation of antral ovarian follicle growth / Interaction With Cumulus Cells And The Zona Pellucida / egg coat formation / positive regulation of humoral immune response / egg coat / structural constituent of egg coat / acrosin binding / positive regulation of acrosome reaction ...positive regulation of type IV hypersensitivity / positive regulation of acrosomal vesicle exocytosis / positive regulation of antral ovarian follicle growth / Interaction With Cumulus Cells And The Zona Pellucida / egg coat formation / positive regulation of humoral immune response / egg coat / structural constituent of egg coat / acrosin binding / positive regulation of acrosome reaction / positive regulation of ovarian follicle development / binding of sperm to zona pellucida / humoral immune response mediated by circulating immunoglobulin / oocyte development / blastocyst formation / regulation of signaling receptor activity / positive regulation of leukocyte migration / detection of maltose stimulus / maltose transport complex / positive regulation of interleukin-4 production / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / positive regulation of T cell proliferation / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / extracellular matrix / positive regulation of inflammatory response / positive regulation of type II interferon production / outer membrane-bounded periplasmic space / carbohydrate binding / collagen-containing extracellular matrix / periplasmic space / receptor ligand activity / negative regulation of DNA-templated transcription / DNA damage response / positive regulation of DNA-templated transcription / extracellular space / membrane / plasma membrane
Similarity search - Function
Zona pellucida, ZP-N domain / : / Zona pellucida domain, conserved site / Zona pellucida, ZP-C domain / ZP domain signature. / Zona pellucida-like domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein ...Zona pellucida, ZP-N domain / : / Zona pellucida domain, conserved site / Zona pellucida, ZP-C domain / ZP domain signature. / Zona pellucida-like domain / Zona pellucida (ZP) 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 / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / : / Maltose/maltodextrin-binding periplasmic protein / Zona pellucida sperm-binding protein 3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsJovine, L. / Monne, M.
Citation
Journal: Nature / Year: 2008
Title: Crystal structure of the ZP-N domain of ZP3 reveals the core fold of animal egg coats
Authors: Monne, M. / Han, L. / Schwend, T. / Burendahl, S. / Jovine, L.
#1: Journal: CELL(CAMBRIDGE,MASS.) / Year: 1980
Title: Mammalian sperm-egg interaction: identification of a glycoprotein in mouse egg zonae pellucidae possessing receptor activity for sperm
Authors: Bleil, J.D. / Wassarman, P.M.
#2: Journal: Febs Lett. / Year: 1992
Title: A large domain common to sperm receptors (Zp2 and Zp3) and TGF-beta type III receptor
Authors: Bork, P. / Sander, C.
#3: Journal: Nat Cell Biol / Year: 2002
Title: The ZP domain is a conserved module for polymerization of extracellular proteins.
Authors: Luca Jovine / Huayu Qi / Zev Williams / Eveline Litscher / Paul M Wassarman /
Abstract: Many eukaryotic extracellular proteins share a sequence of unknown function, called the zona pellucida (ZP) domain. Among these proteins are the mammalian sperm receptors ZP2 and ZP3, non-mammalian ...Many eukaryotic extracellular proteins share a sequence of unknown function, called the zona pellucida (ZP) domain. Among these proteins are the mammalian sperm receptors ZP2 and ZP3, non-mammalian egg coat proteins, Tamm-Horsfall protein (THP), glycoprotein-2 (GP-2), alpha- and beta-tectorins, transforming growth factor (TGF)-beta receptor III and endoglin, DMBT-1 (deleted in malignant brain tumour-1), NompA (no-mechanoreceptor-potential-A), Dumpy and cuticlin-1 (refs 1,2). Here, we report that the ZP domain of ZP2, ZP3 and THP is responsible for polymerization of these proteins into filaments of similar supramolecular structure. Most ZP domain proteins are synthesized as precursors with carboxy-terminal transmembrane domains or glycosyl phosphatidylinositol (GPI) anchors. Our results demonstrate that the C-terminal transmembrane domain and short cytoplasmic tail of ZP2 and ZP3 are not required for secretion, but are essential for assembly. Finally, we suggest a molecular basis for dominant human hearing disorders caused by point mutations within the ZP domain of alpha-tectorin.
#4: Journal: Proc Natl Acad Sci U S A / Year: 2004
Title: A duplicated motif controls assembly of zona pellucida domain proteins.
Authors: Luca Jovine / Huayu Qi / Zev Williams / Eveline S Litscher / Paul M Wassarman /
Abstract: Many secreted eukaryotic glycoproteins that play fundamental roles in development, hearing, immunity, and cancer polymerize into filaments and extracellular matrices through zona pellucida (ZP) ...Many secreted eukaryotic glycoproteins that play fundamental roles in development, hearing, immunity, and cancer polymerize into filaments and extracellular matrices through zona pellucida (ZP) domains. ZP domain proteins are synthesized as precursors containing C-terminal propeptides that are cleaved at conserved sites. However, the consequences of this processing and the mechanism by which nascent proteins assemble are unclear. By microinjection of mutated DNA constructs into growing oocytes and mammalian cell transfection, we have identified a conserved duplicated motif [EHP (external hydrophobic patch)/IHP (internal hydrophobic patch)] regulating the assembly of mouse ZP proteins. Whereas the transmembrane domain (TMD) of ZP3 can be functionally replaced by an unrelated TMD, mutations in either EHP or IHP do not hinder secretion of full-length ZP3 but completely abolish its assembly. Because mutants truncated before the TMD are not processed, we conclude that the conserved TMD of mammalian ZP proteins does not engage them in specific interactions but is essential for C-terminal processing. Cleavage of ZP precursors results in loss of the EHP, thereby activating secreted polypeptides to assemble by using the IHP within the ZP domain. Taken together, these findings suggest a general mechanism for assembly of ZP domain proteins.
#5: Journal: Annu Rev Biochem / Year: 2005
Title: Zona pellucida domain proteins.
Authors: Luca Jovine / Costel C Darie / Eveline S Litscher / Paul M Wassarman /
Abstract: Many eukaryotic proteins share a sequence designated as the zona pellucida (ZP) domain. This structural element, present in extracellular proteins from a wide variety of organisms, from nematodes to ...Many eukaryotic proteins share a sequence designated as the zona pellucida (ZP) domain. This structural element, present in extracellular proteins from a wide variety of organisms, from nematodes to mammals, consists of approximately 260 amino acids with eight conserved cysteine (Cys) residues and is located close to the C terminus of the polypeptide. ZP domain proteins are often glycosylated, modular structures consisting of multiple types of domains. Predictions can be made about some of the structural features of the ZP domain and ZP domain proteins. The functions of ZP domain proteins vary tremendously, from serving as structural components of egg coats, appendicularian mucous houses, and nematode dauer larvae, to serving as mechanotransducers in flies and receptors in mammals and nonmammals. Generally, ZP domain proteins are present in filaments and/or matrices, which is consistent with the role of the domain in protein polymerization. A general mechanism for assembly of ZP domain proteins has been presented. It is likely that the ZP domain plays a common role despite its presence in proteins of widely diverse functions.
#6: Journal: Bmc Biochem. / Year: 2006
Title: The PLAC1-homology region of the ZP domain is sufficient for protein polymerisation
Authors: Jovine, L. / Janssen, W.G. / Litscher, E.S. / Wassarman, P.M.
History
DepositionMay 14, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
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Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_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.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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED
Remark 40MOLPROBITY STRUCTURE VALIDATION PROGRAMS: MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS: I.W.DAVIS,V. ...MOLPROBITY STRUCTURE VALIDATION PROGRAMS: MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS: I.W.DAVIS,V.B.CHEN, R.M.IMMORMINO, J.J.HEADD,W.B.ARENDALL,J.M.WORD AUTHORS: I.W.DAVIS,A.LEAVER-FAY,V.B.CHEN,J.N.BLOCK, G.J.KAPRAL,X.WANG,L.W.MURRAY,W.B.ARENDALL, J.SNOEYINK,J.S.RICHARDSON,D.C.RICHARDSON REFERENCE: MOLPROBITY: ALL-ATOM CONTACTS AND STRUCTURE VALIDATION FOR PROTEINS AND NUCLEIC ACIDS NUCLEIC ACIDS RESEARCH. 2007;35:W375-83.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0789
Polymers52,9491
Non-polymers1,1298
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.040, 95.120, 141.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-485-

CD

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Components

#1: Protein Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3 / Maltose-binding protein/ZP3 ZP-N domain chimera / MBP / Zona pellucida glycoprotein ZP3 / Sperm ...Maltose-binding protein/ZP3 ZP-N domain chimera / MBP / Zona pellucida glycoprotein ZP3 / Sperm receptor / Zona pellucida protein C


Mass: 52948.945 Da / Num. of mol.: 1
Fragment: ZP3 ZP-N domain, UNP residues 27-393, UNP residues 42-143
Mutation: I3T, E360A, K363A, D364A, R368N
Source method: isolated from a genetically manipulated source
Details: This protein is a chimera. Residues 2-368 are from E. COLI maltose binding protein (MBP), correspond to residues 27-393 of swiss-prot database entry P0AEX9 and contain mutations I3T, E360A, ...Details: This protein is a chimera. Residues 2-368 are from E. COLI maltose binding protein (MBP), correspond to residues 27-393 of swiss-prot database entry P0AEX9 and contain mutations I3T, E360A, K363A, D364A, R368N (corresponding to I28T, E385A, K388A, D389A AND R393N in P0AEX9). Residues 372-473 are from mouse ZP3 protein and correspond to residues 42-143 of swiss-prot database entry P10761.
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Mus musculus (house mouse)
Cellular location: Extracellular matrix / Gene: Zp3, Zp-3, Zpc / Plasmid: PLJMBP4C, PLJDIS1 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P0AEX9, UniProt: P10761
#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-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd

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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: 2.94 Å3/Da / Density % sol: 58.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Sample: 15mg/ml protein in 0.05M sodium chloride, 0.01M tris-HCL, PH7.2, 0.001M maltose. Reservoir: 1.0M sodium acetate, 0,1M sodium HEPES, PH7.5, 0.05M cadmium sulfate. Sample to reservoir ...Details: Sample: 15mg/ml protein in 0.05M sodium chloride, 0.01M tris-HCL, PH7.2, 0.001M maltose. Reservoir: 1.0M sodium acetate, 0,1M sodium HEPES, PH7.5, 0.05M cadmium sulfate. Sample to reservoir ratio in drop: 1:1, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9535 / Wavelength: 0.9535 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 6, 2006
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9535 Å / Relative weight: 1
ReflectionResolution: 2.9→16.5 Å / Num. all: 14197 / Num. obs: 14196 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Biso Wilson estimate: 92.46 Å2 / Rsym value: 0.047 / Net I/σ(I): 33.1
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 2334 / Rsym value: 0.754 / % possible all: 100

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Processing

Software
NameClassification
PHASERphasing
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ENSEMBLE DERIVED FROM PDB ENTRIES 1MG1 (chain A), 1NMU (chain C), 1T0K (chain A), 1YTV (chain B), 3MBP (chain A), 4MBP (chain A)

1mg1

1nmu

1t0k

1ytv

3mbp

4mbp


Resolution: 2.9→16.5 Å / SU ML: 0.38 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.66 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 844 5.95 %Random
Rwork0.19 ---
obs0.1922 14194 100 %-
all-14296 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.453 Å2 / ksol: 0.299 e/Å3
Displacement parametersBiso mean: 113.79 Å2
Baniso -1Baniso -2Baniso -3
1--7.6478 Å20 Å20 Å2
2--0.674 Å20 Å2
3---6.9738 Å2
Refinement stepCycle: LAST / Resolution: 2.9→16.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3629 0 30 0 3659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083737
X-RAY DIFFRACTIONf_angle_d0.645079
X-RAY DIFFRACTIONf_dihedral_angle_d13.7671356
X-RAY DIFFRACTIONf_chiral_restr0.041572
X-RAY DIFFRACTIONf_plane_restr0.004656
LS refinement shellResolution: 2.9→3.08 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3514 154 -
Rwork0.3106 2180 -
obs--100 %
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)
16.83343.026-0.22282.9915-2.03833.8905-0.13740.58121.59330.10770.12260.48390.10610.06110.03150.5336-0.01620.08360.50040.32120.813-37.430625.9308-21.8419
24.35171.0369-0.51995.23790.74741.5488-0.19461.11570.345-0.22640.0644-1.3146-0.07880.73990.0920.5052-0.15890.15110.98510.07630.9003-11.702515.1399-20.8062
33.40851.38551.07312.17060.5431.6853-0.23741.02460.7525-0.03350.24240.1719-0.0420.34390.01030.3942-0.10190.22770.51910.2990.5542-27.528821.4099-24.6022
46.13342.3622.55587.30091.8358-0.0590.41640.0914-0.20370.439-0.1819-0.05240.3417-0.0875-0.20350.48160.0237-0.00050.4071-0.05760.2568-35.9856-4.804-14.3636
52.5856-0.2528-0.88225.1064.21595.1845-0.12090.31-0.3910.48010.53130.0060.01841.2452-0.43120.50280.1734-0.05950.6547-0.22630.478-28.6335-10.0574-19.237
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND (RESID 5:113 OR RESID 482:482 OR RESID 487:488))A5 - 474
2X-RAY DIFFRACTION1(CHAIN A AND (RESID 5:113 OR RESID 482:482 OR RESID 487:488))A482
3X-RAY DIFFRACTION1(CHAIN A AND (RESID 5:113 OR RESID 482:482 OR RESID 487:488))A487 - 488
4X-RAY DIFFRACTION2(CHAIN A AND (RESID 114:258 OR RESID 484:484 OR RESID 489:489))A114 - 258
5X-RAY DIFFRACTION2(CHAIN A AND (RESID 114:258 OR RESID 484:484 OR RESID 489:489))A484
6X-RAY DIFFRACTION2(CHAIN A AND (RESID 114:258 OR RESID 484:484 OR RESID 489:489))A489
7X-RAY DIFFRACTION3(CHAIN A AND RESID 259:372)A259 - 372
8X-RAY DIFFRACTION4(CHAIN A AND (RESID 373:446 OR RESID 483:483))A373 - 446
9X-RAY DIFFRACTION4(CHAIN A AND (RESID 373:446 OR RESID 483:483))A483
10X-RAY DIFFRACTION5(CHAIN A AND (RESID 447:474 OR RESID 486:486))A447 - 474
11X-RAY DIFFRACTION5(CHAIN A AND (RESID 447:474 OR RESID 486:486))A486

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