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- PDB-5hzv: Crystal structure of the zona pellucida module of human endoglin/CD105 -

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Entry
Database: PDB / ID: 5hzv
TitleCrystal structure of the zona pellucida module of human endoglin/CD105
ComponentsMaltose-binding periplasmic protein,Endoglin
KeywordsSIGNALING PROTEIN / ZONA PELLUCIDA DOMAIN / ANGIOGENESIS / GLYCOPROTEIN / RECEPTOR
Function / homology
Function and homology information


extracellular matrix constituent secretion / atrioventricular canal morphogenesis / detection of hypoxia / endothelial microparticle / venous blood vessel morphogenesis / dorsal aorta morphogenesis / positive regulation of vascular associated smooth muscle cell differentiation / atrial cardiac muscle tissue morphogenesis / cell migration involved in endocardial cushion formation / vascular associated smooth muscle cell development ...extracellular matrix constituent secretion / atrioventricular canal morphogenesis / detection of hypoxia / endothelial microparticle / venous blood vessel morphogenesis / dorsal aorta morphogenesis / positive regulation of vascular associated smooth muscle cell differentiation / atrial cardiac muscle tissue morphogenesis / cell migration involved in endocardial cushion formation / vascular associated smooth muscle cell development / central nervous system vasculogenesis / epithelial to mesenchymal transition involved in endocardial cushion formation / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / cardiac ventricle morphogenesis / regulation of transforming growth factor beta receptor signaling pathway / galactose binding / cardiac atrium morphogenesis / smooth muscle tissue development / type II transforming growth factor beta receptor binding / activin binding / type I transforming growth factor beta receptor binding / regulation of phosphorylation / outflow tract septum morphogenesis / ventricular trabecula myocardium morphogenesis / glycosaminoglycan binding / positive regulation of BMP signaling pathway / transforming growth factor beta binding / artery morphogenesis / endocardial cushion morphogenesis / branching involved in blood vessel morphogenesis / negative regulation of SMAD protein signal transduction / detection of maltose stimulus / maltose transport complex / signaling receptor activator activity / negative regulation of endothelial cell proliferation / heart looping / positive regulation of systemic arterial blood pressure / carbohydrate transport / positive regulation of collagen biosynthetic process / positive regulation of SMAD protein signal transduction / extracellular matrix disassembly / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / BMP signaling pathway / regulation of cell adhesion / vasculogenesis / coreceptor activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / transforming growth factor beta receptor signaling pathway / ATP-binding cassette (ABC) transporter complex / negative regulation of cell migration / cell chemotaxis / cell motility / negative regulation of transforming growth factor beta receptor signaling pathway / wound healing / bone development / cellular response to mechanical stimulus / positive regulation of angiogenesis / transmembrane signaling receptor activity / cell migration / regulation of cell population proliferation / outer membrane-bounded periplasmic space / periplasmic space / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / cell adhesion / nuclear body / response to xenobiotic stimulus / external side of plasma membrane / negative regulation of gene expression / focal adhesion / DNA damage response / positive regulation of gene expression / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / membrane / plasma membrane
Similarity search - Function
ZP-C 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 / Endoglin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBokhove, M. / Saito, T. / Jovine, L.
Funding support Sweden, 7items
OrganizationGrant numberCountry
Karolinska Institutet Sweden
Center for Biosciences Sweden
Swedish Research Council2012-5093 Sweden
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 Rep / Year: 2017
Title: Structural Basis of the Human Endoglin-BMP9 Interaction: Insights into BMP Signaling and HHT1.
Authors: Saito, T. / Bokhove, M. / Croci, R. / Zamora-Caballero, S. / Han, L. / Letarte, M. / de Sanctis, D. / Jovine, L.
#1: Journal: J. Biol. Chem. / Year: 1990
Title: Primary structure of endoglin, an RGD-containing glycoprotein of human endothelial cells.
Authors: Gougos, A. / Letarte, 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: 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.
#4: Journal: Cell / Year: 2010
Title: Insights into egg coat assembly and egg-sperm interaction from the X-ray structure of full-length ZP3.
Authors: Ling Han / Magnus Monné / Hiroki Okumura / Thomas Schwend / Amy L Cherry / David Flot / Tsukasa Matsuda / Luca Jovine /
Abstract: ZP3, a major component of the zona pellucida (ZP) matrix coating mammalian eggs, is essential for fertilization by acting as sperm receptor. By retaining a propeptide that contains a polymerization- ...ZP3, a major component of the zona pellucida (ZP) matrix coating mammalian eggs, is essential for fertilization by acting as sperm receptor. By retaining a propeptide that contains a polymerization-blocking external hydrophobic patch (EHP), we determined the crystal structure of an avian homolog of ZP3 at 2.0 Å resolution. The structure unveils the fold of a complete ZP domain module in a homodimeric arrangement required for secretion and reveals how EHP prevents premature incorporation of ZP3 into the ZP. This suggests mechanisms underlying polymerization and how local structural differences, reflected by alternative disulfide patterns, control the specificity of ZP subunit interaction. Close relative positioning of a conserved O-glycan important for sperm binding and the hypervariable, positively selected C-terminal region of ZP3 suggests a concerted role in the regulation of species-restricted gamete recognition. Alternative conformations of the area around the O-glycan indicate how sperm binding could trigger downstream events via intramolecular signaling.
#5: Journal: Proc Natl Acad Sci U S A / Year: 2016
Title: A structured interdomain linker directs self-polymerization of human uromodulin.
Authors: Marcel Bokhove / Kaoru Nishimura / Martina Brunati / Ling Han / Daniele de Sanctis / Luca Rampoldi / Luca Jovine /
Abstract: Uromodulin (UMOD)/Tamm-Horsfall protein, the most abundant human urinary protein, plays a key role in chronic kidney diseases and is a promising therapeutic target for hypertension. Via its bipartite ...Uromodulin (UMOD)/Tamm-Horsfall protein, the most abundant human urinary protein, plays a key role in chronic kidney diseases and is a promising therapeutic target for hypertension. Via its bipartite zona pellucida module (ZP-N/ZP-C), UMOD forms extracellular filaments that regulate kidney electrolyte balance and innate immunity, as well as protect against renal stones. Moreover, salt-dependent aggregation of UMOD filaments in the urine generates a soluble molecular net that captures uropathogenic bacteria and facilitates their clearance. Despite the functional importance of its homopolymers, no structural information is available on UMOD and how it self-assembles into filaments. Here, we report the crystal structures of polymerization regions of human UMOD and mouse ZP2, an essential sperm receptor protein that is structurally related to UMOD but forms heteropolymers. The structure of UMOD reveals that an extensive hydrophobic interface mediates ZP-N domain homodimerization. This arrangement is required for filament formation and is directed by an ordered ZP-N/ZP-C linker that is not observed in ZP2 but is conserved in the sequence of deafness/Crohn's disease-associated homopolymeric glycoproteins α-tectorin (TECTA) and glycoprotein 2 (GP2). Our data provide an example of how interdomain linker plasticity can modulate the function of structurally similar multidomain proteins. Moreover, the architecture of UMOD rationalizes numerous pathogenic mutations in both UMOD and TECTA genes.
History
DepositionFeb 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
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Revision 1.2Aug 23, 2017Group: Database references / Source and taxonomy / Structure summary
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Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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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.pdbx_synonyms / _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 / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Endoglin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6633
Polymers68,2281
Non-polymers4342
Water27015
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint2 kcal/mol
Surface area27770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.160, 125.160, 88.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Maltose-binding periplasmic protein,Endoglin / MBP / MMBP / Maltodextrin-binding protein


Mass: 68228.398 Da / Num. of mol.: 1
Mutation: D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND ...Mutation: D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N
Source method: isolated from a genetically manipulated source
Details: THIS PROTEIN IS A CHIMERA. RESIDUES 368-734 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 27-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS D449A, ...Details: THIS PROTEIN IS A CHIMERA. RESIDUES 368-734 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 27-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N (CORRESPONDING TO D108A, K109A, E198A, N199A, A241H, K245H, K265A, A338V, I343V, E385A, E388A, D389A AND R393N IN P0AEX9). RESIDUES 738-981 ARE FROM HUMAN ENDOGLIN PROTEIN AND CORRESPOND TO RESIDUES 338-581 OF SWISS-PROT DATABASE ENTRY P17813. SUBTRACTING 400 FROM THE PDB ENTRY RESIDUE NUMBERING RESULTS IN THE NUMBERING ACCORDING TO UNIPROT ENTRY P17813.
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K12 / Cell: ENDOTHELIAL / Gene: malE, b4034, JW3994, ENG, END / Plasmid: pHLsec / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P0AEX9, UniProt: P17813
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
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: 2.94 Å3/Da / Density % sol: 58.2 % / Description: Hexagonal rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 11.5% equal mixture of MPD, PEG 1000 and PEG 3350 (1:1:1), MES/imidazole mix
PH range: 5.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2015
RadiationMonochromator: Si Single Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→29.51 Å / Num. obs: 21583 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 72.174 Å2 / Rsym value: 0.062 / Net I/σ(I): 9.43
Reflection shellResolution: 2.69→2.76 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 0.99 / % possible all: 85.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDS(Jun 17, 2015)data reduction
XSCALE(Jun 17, 2015)data scaling
PHASER(2.5.6)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SEX

3sex


Resolution: 2.7→29.5037 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1138 5.31 %Random selection
Rwork0.2318 ---
obs0.234 21429 98.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→29.5037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4582 0 29 15 4626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024719
X-RAY DIFFRACTIONf_angle_d0.5346414
X-RAY DIFFRACTIONf_dihedral_angle_d10.6332844
X-RAY DIFFRACTIONf_chiral_restr0.041727
X-RAY DIFFRACTIONf_plane_restr0.004823
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
2.7005-2.82340.44291254.780.4031249297
2.8234-2.97210.40351435.30.3637255399
2.9721-3.15810.36681495.550.3246253499
3.1581-3.40160.34061134.190.2837258299
3.4016-3.74330.28911575.880.2516251399
3.7433-4.28360.23651465.420.2187255099
4.2836-5.39150.21721525.70.1832251698
5.3915-29.50370.24831535.660.1829255197
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
11.2148-0.7364-1.09542.92131.80183.253-0.1450.1242-0.03730.2215-0.0513-0.07760.2670.1346-0.00390.8027-0.0504-0.01450.5983-0.00060.7139mMBP10.507883.751356.5438
21.481-0.7179-0.88371.50770.52891.26730.01580.25710.13530.094-0.15670.2022-0.6051-0.134-00.78460.1771-0.06160.97560.00670.7623ZP-N40.991150.116272.0674
30.4743-0.04590.05541.19650.46370.86320.05110.2044-0.43-0.41370.00810.72610.17890.1638-0.00010.98020.0858-0.00870.9352-0.0491.13ZP-C39.324415.256763.087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 844:976)
2X-RAY DIFFRACTION2chain A and (resid 743:843)
3X-RAY DIFFRACTION3chain A and (resid 844:976)

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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