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- PDB-5hzw: Crystal structure of the orphan region of human endoglin/CD105 in... -

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Entry
Database: PDB / ID: 5hzw
TitleCrystal structure of the orphan region of human endoglin/CD105 in complex with BMP9
Components
  • Growth/differentiation factor 2
  • Maltose-binding periplasmic protein,Endoglin
KeywordsSIGNALING PROTEIN / ORPHAN DOMAIN / ANGIOGENESIS / GLYCOPROTEIN / RECEPTOR
Function / homology
Function and homology information


atrioventricular canal morphogenesis / detection of hypoxia / endothelial microparticle / venous blood vessel morphogenesis / dorsal aorta morphogenesis / cell migration involved in endocardial cushion formation / vascular associated smooth muscle cell development / atrial cardiac muscle tissue morphogenesis / positive regulation of vascular associated smooth muscle cell differentiation / positive regulation of epithelial cell differentiation ...atrioventricular canal morphogenesis / detection of hypoxia / endothelial microparticle / venous blood vessel morphogenesis / dorsal aorta morphogenesis / cell migration involved in endocardial cushion formation / vascular associated smooth muscle cell development / atrial cardiac muscle tissue morphogenesis / positive regulation of vascular associated smooth muscle cell differentiation / positive regulation of epithelial cell differentiation / 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 / positive regulation of cartilage development / regulation of transforming growth factor beta receptor signaling pathway / galactose binding / positive regulation of endothelial cell differentiation / cardiac atrium morphogenesis / smooth muscle tissue development / type II transforming growth factor beta receptor binding / activin binding / cellular response to BMP stimulus / Signaling by BMP / type I transforming growth factor beta receptor binding / regulation of phosphorylation / glycosaminoglycan binding / activin receptor signaling pathway / ventricular trabecula myocardium morphogenesis / positive regulation of BMP signaling pathway / positive regulation of bicellular tight junction assembly / outflow tract septum morphogenesis / transforming growth factor beta binding / cartilage development / blood vessel morphogenesis / negative regulation of endothelial cell migration / artery morphogenesis / endocardial cushion morphogenesis / branching involved in blood vessel morphogenesis / positive regulation of Notch signaling pathway / heart looping / detection of maltose stimulus / negative regulation of endothelial cell proliferation / negative regulation of DNA replication / maltose transport complex / negative regulation of SMAD protein signal transduction / positive regulation of systemic arterial blood pressure / carbohydrate transport / signaling receptor activator activity / negative regulation of blood vessel endothelial cell migration / positive regulation of SMAD protein signal transduction / extracellular matrix disassembly / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / BMP signaling pathway / vasculogenesis / regulation of cell adhesion / coreceptor activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / positive regulation of endothelial cell proliferation / transforming growth factor beta receptor signaling pathway / ATP-binding cassette (ABC) transporter complex / ossification / negative regulation of cell migration / negative regulation of angiogenesis / protein serine/threonine kinase activator activity / cytokine activity / cell chemotaxis / positive regulation of interleukin-8 production / growth factor activity / cell motility / negative regulation of transforming growth factor beta receptor signaling pathway / wound healing / negative regulation of cell growth / positive regulation of angiogenesis / osteoblast differentiation / transmembrane signaling receptor activity / cell migration / regulation of cell population proliferation / outer membrane-bounded periplasmic space / angiogenesis / intracellular iron ion homeostasis / transcription by RNA polymerase II / response to hypoxia / periplasmic space / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / cell adhesion / nuclear body / negative regulation of gene expression / external side of plasma membrane / focal adhesion / DNA damage response / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / cell surface / negative regulation of transcription by RNA polymerase II / protein homodimerization activity
Similarity search - Function
TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine-knot cytokine ...TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine-knot cytokine / 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 / Maltose/maltodextrin-binding periplasmic protein / Endoglin / Growth/differentiation factor 2
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.451 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: J. Cell. Sci. / Year: 2007
Title: BMP-9 signals via ALK1 and inhibits bFGF-induced endothelial cell proliferation and VEGF-stimulated angiogenesis.
Authors: Scharpfenecker, M. / van Dinther, M. / Liu, Z. / van Bezooijen, R.L. / Zhao, Q. / Pukac, L. / Lowik, C.W. / ten Dijke, P.
#3: Journal: J. Biol. Chem. / Year: 2011
Title: Soluble endoglin specifically binds bone morphogenetic proteins 9 and 10 via its orphan domain, inhibits blood vessel formation, and suppresses tumor growth.
Authors: Castonguay, R. / Werner, E.D. / Matthews, R.G. / Presman, E. / Mulivor, A.W. / Solban, N. / Sako, D. / Pearsall, R.S. / Underwood, K.W. / Seehra, J. / Kumar, R. / Grinberg, A.V.
#4: Journal: PLoS ONE / Year: 2012
Title: Structural and functional insights into endoglin ligand recognition and binding.
Authors: Alt, A. / Miguel-Romero, L. / Donderis, J. / Aristorena, M. / Blanco, F.J. / Round, A. / Rubio, V. / Bernabeu, C. / Marina, A.
#5: Journal: PLoS ONE / Year: 2012
Title: Endoglin requirement for BMP9 signaling in endothelial cells reveals new mechanism of action for selective anti-endoglin antibodies.
Authors: Nolan-Stevaux, O. / Zhong, W. / Culp, S. / Shaffer, K. / Hoover, J. / Wickramasinghe, D. / Ruefli-Brasse, A.
History
DepositionFeb 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.page_last ..._citation.country / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_symm_contact / 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.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _struct_asym.entity_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
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 2.2Oct 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
B: Growth/differentiation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0295
Polymers87,2442
Non-polymers7853
Water00
1
A: Maltose-binding periplasmic protein,Endoglin
B: Growth/differentiation factor 2
hetero molecules

A: Maltose-binding periplasmic protein,Endoglin
B: Growth/differentiation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,05810
Polymers174,4884
Non-polymers1,5696
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Buried area2780 Å2
ΔGint1 kcal/mol
Surface area34640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.245, 211.245, 53.164
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

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


Mass: 75141.164 Da / Num. of mol.: 1
Fragment: UNP Residues 27-393,UNP Residues 25-337,UNP Residues 27-393,UNP Residues 25-337
Mutation: I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N
Source method: isolated from a genetically manipulated source
Details: THIS PROTEIN IS A CHIMERA. RESIDUES 56-422 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 27-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS I57T, ...Details: THIS PROTEIN IS A CHIMERA. RESIDUES 56-422 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 27-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A AND R422N (CORRESPONDING TO I28T, D108A, K109A, E198A, N199A, A241H, K245H, K265A, A338V, I343V, E385A, E388A, D389A AND R393N IN P0AEX9). RESIDUES 426-737 ARE FROM HUMAN ENDOGLIN PROTEIN AND CORRESPOND TO RESIDUES 26-337 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 K12 (bacteria), (gene. exp.) Homo sapiens (human)
Cell: Endothelial / Gene: malE, b4034, JW3994, ENG, END / Plasmid: pHLsec / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P0AEX9, UniProt: P17813
#2: Protein Growth/differentiation factor 2 / GDF-2 / Bone morphogenetic protein 9 / BMP-9


Mass: 12102.971 Da / Num. of mol.: 1 / Fragment: UNP residues 320-429
Source method: isolated from a genetically manipulated source
Details: Mature BMP9 / Source: (gene. exp.) Homo sapiens (human) / Gene: GDF2, BMP9 / Plasmid: pHLsec / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q9UK05
#3: 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
#4: 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.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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: 4.14 Å3/Da / Density % sol: 70.3 % / Description: Hexagonal Bipyramid
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.1 M AMMONIUM TARTRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97938 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2014
RadiationMonochromator: Si Single Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 4.301→52.811 Å / Num. obs: 9558 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 219 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.395 / Net I/σ(I): 3.5
Reflection shellResolution: 4.301→4.81 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 0.6 / CC1/2: 0.259 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DIALS1.dev.176data reduction
Aimless0.525data scaling
PHASER(2.5.6)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SEX, 5I04, 5I05

3sex

5i04

5i05


Resolution: 4.451→52.811 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3181 847 9.84 %Random selection
Rwork0.2855 ---
obs0.2888 8611 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.451→52.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5934 0 51 0 5985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046143
X-RAY DIFFRACTIONf_angle_d0.6348377
X-RAY DIFFRACTIONf_dihedral_angle_d9.3253678
X-RAY DIFFRACTIONf_chiral_restr0.044951
X-RAY DIFFRACTIONf_plane_restr0.0051075
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.4511-4.72980.39031160.36581290X-RAY DIFFRACTION100
4.7298-5.09470.33821410.34461268X-RAY DIFFRACTION100
5.0947-5.60690.36971290.34911287X-RAY DIFFRACTION100
5.6069-6.4170.40031510.38141286X-RAY DIFFRACTION100
6.417-8.08010.33561440.31911298X-RAY DIFFRACTION100
8.0801-52.81490.27061660.22291336X-RAY DIFFRACTION100
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)
11.43140.94441.15153.1155-0.06721.57780.04780.20050.81660.0389-0.21020.1406-0.3937-0.2941-02.86030.07180.26833.0418-0.02753.078927.6408-32.5548-8.3505
25.07740.87931.30442.2122-0.19522.37070.22460.004-0.74330.15010.13850.0678-0.29070.315603.0278-0.00210.24072.8563-0.04982.903620.3422-60.48686.3522
30.06430.04660.06580.03110.04890.0554-0.1402-0.78110.8171-0.1461-0.3284-0.1238-0.88470.2915-03.61590.3354-0.15643.8743-0.14764.124239.1704-90.105942.1687
40.3982-0.0135-0.50810.0875-0.03360.49070.1737-0.7223-1.0691.69010.95163.032-0.2809-0.81610.00213.06660.3664-0.53052.877-0.05953.130146.8781-90.214840.336
50.96440.68350.80861.2150.83020.6837-0.29061.25640.63160.4217-1.4158-1.43460.2064-0.4996-03.03770.2723-0.49423.4795-0.24883.223746.8046-83.268233.7533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 59:388 or resi 1000)
2X-RAY DIFFRACTION2chain 'A' and (resid 389:730 or resi 801 or resi 810)
3X-RAY DIFFRACTION3chain 'B' and (resid 6:16)
4X-RAY DIFFRACTION4chain 'B' and (resid 17:64)
5X-RAY DIFFRACTION5chain 'B' and (resid 65:110)

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