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- PDB-5i04: Crystal structure of the orphan region of human endoglin/CD105 -

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Entry
Database: PDB / ID: 5i04
TitleCrystal structure of the orphan region of human endoglin/CD105
ComponentsMaltose-binding periplasmic protein,Endoglin
KeywordsSIGNALING PROTEIN / ORPHAN DOMAIN / ANGIOGENESIS / GLYCOPROTEIN / RECEPTOR
Function / homology
Function and homology information


venous blood vessel morphogenesis / central nervous system vasculogenesis / atrioventricular canal morphogenesis / detection of hypoxia / endothelial microparticle / dorsal aorta morphogenesis / atrial cardiac muscle tissue morphogenesis / vascular associated smooth muscle cell development / cardiac atrium morphogenesis / cardiac ventricle morphogenesis ...venous blood vessel morphogenesis / central nervous system vasculogenesis / atrioventricular canal morphogenesis / detection of hypoxia / endothelial microparticle / dorsal aorta morphogenesis / atrial cardiac muscle tissue morphogenesis / vascular associated smooth muscle cell development / cardiac atrium morphogenesis / cardiac ventricle morphogenesis / positive regulation of vascular associated smooth muscle cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / regulation of transforming growth factor beta receptor signaling pathway / galactose binding / smooth muscle tissue development / type II transforming growth factor beta receptor binding / activin binding / ventricular trabecula myocardium morphogenesis / glycosaminoglycan binding / type I transforming growth factor beta receptor binding / positive regulation of BMP signaling pathway / outflow tract septum morphogenesis / artery morphogenesis / branching involved in blood vessel morphogenesis / endocardial cushion morphogenesis / transforming growth factor beta binding / heart looping / negative regulation of endothelial cell proliferation / negative regulation of SMAD protein signal transduction / detection of maltose stimulus / positive regulation of systemic arterial blood pressure / vasculogenesis / carbohydrate transport / positive regulation of SMAD protein signal transduction / extracellular matrix disassembly / signaling receptor activator activity / BMP signaling pathway / regulation of cell adhesion / transforming growth factor beta receptor signaling pathway / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / coreceptor activity / ATP-binding cassette (ABC) transporter complex / negative regulation of cell migration / cell motility / negative regulation of transforming growth factor beta receptor signaling pathway / wound healing / cell chemotaxis / transmembrane signaling receptor activity / regulation of cell population proliferation / cell migration / outer membrane-bounded periplasmic space / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to hypoxia / cell adhesion / periplasmic space / signaling receptor complex / negative regulation of gene expression / external side of plasma membrane / focal adhesion / DNA damage response / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / cell surface / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / : / membrane / identical protein binding / plasma membrane
Similarity search - Function
: / TGFBR3-like, N-terminal 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 / Endoglin
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsSaito, T. / Bokhove, M. / de Sanctis, D. / 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. 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.
#3: 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.
#4: 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: RCSB / 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: 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_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.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.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
Revision 2.2Oct 16, 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,Endoglin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2686
Polymers75,2541
Non-polymers1,0145
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint19 kcal/mol
Surface area29150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.150, 114.150, 120.620
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: 75254.336 Da / Num. of mol.: 1
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, ...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,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,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,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,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,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,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,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 K-12 (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: 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: 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.: 1
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
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.02 Å3/Da / Density % sol: 57.8 % / Description: Droplet
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG 1000, 0.1 M TRIS-HCL / PH range: 7.0-8.5

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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 / Detector: PIXEL / Date: Sep 10, 2014
RadiationMonochromator: Si Single Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.42→45.74 Å / Num. obs: 33737 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 70.03 Å2 / Rsym value: 0.046 / Net I/σ(I): 11.76
Reflection shellResolution: 2.42→2.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.811 / Mean I/σ(I) obs: 1.25 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: 000)refinement
XDS(VERSION November 3, 2014)data reduction
XSCALE(VERSION November 3, 2014 BUILT=20141103)data scaling
PHASER(2.5.6)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SEX, 3SET, 4WRN

3sex

3set

4wrn


Resolution: 2.42→45.737 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 35.15
RfactorNum. reflection% reflectionSelection details
Rfree0.2627 1636 4.85 %Random selection
Rwork0.2202 ---
obs0.2223 33699 99.05 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 76.6 Å2
Refinement stepCycle: LAST / Resolution: 2.42→45.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5117 0 67 26 5210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035309
X-RAY DIFFRACTIONf_angle_d0.5547226
X-RAY DIFFRACTIONf_dihedral_angle_d10.8183175
X-RAY DIFFRACTIONf_chiral_restr0.042822
X-RAY DIFFRACTIONf_plane_restr0.004928
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
2.42-2.49120.4391194.280.3889266198
2.4912-2.57160.39961515.450.3696261899
2.5716-2.66350.39981545.460.353266999
2.6635-2.77020.3761284.580.3336266599
2.7702-2.89620.35381154.130.3189266799
2.8962-3.04890.36781595.660.2885264999
3.0489-3.23990.29761194.240.2675268599
3.2399-3.48990.29221314.670.2413267399
3.4899-3.8410.28511425.040.20562674100
3.841-4.39640.21271455.060.182719100
4.3964-5.53750.18841475.230.1589266499
5.5375-45.74530.2291264.430.1866271998
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)Details (eV)Origin x (Å)Origin y (Å)Origin z (Å)
10.2049-0.24670.12751.2947-0.14460.5482-0.10680.09790.0610.10680.17630.06870.07730.41210.00020.43390.0052-0.00380.80860.01230.5765mMBP33.396658.638280.0463
20.6940.14460.11520.74970.05521.05180.0476-0.0479-0.03770.00670.00560.02780.0317-0.1893-00.4610.0477-0.0210.684-0.01490.5176Orphan Domain I34.759430.874154.9932
30.729-0.0937-0.37350.78830.28321.0039-0.03420.08540.0211-0.04990.0967-0.059-0.11640.013600.4936-0.006-0.00320.45770.01050.5382Orphan Domain II64.592630.373269.293
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resi 54:425) or chain X
2X-RAY DIFFRACTION2chain A and (resi 426:446 or resi 600:728)
3X-RAY DIFFRACTION3chain A and (resi 447:599 or resi 1000)

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