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- PDB-4uhy: Crystal structure of the human RGMA-BMP2 complex -

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Basic information

Entry
Database: PDB / ID: 4uhy
TitleCrystal structure of the human RGMA-BMP2 complex
Components
  • BONE MORPHOGENETIC PROTEIN 2
  • REPULSIVE GUIDANCE MOLECULE A
KeywordsSIGNALING PROTEIN / BONE MORPHOGENETIC PROTEIN PATHWAY / HEMOJUVELIN / MORPHOGEN / AXON GUIDANCE / CELL SURFACE RECEPTOR SIGNALING
Function / homology
Function and homology information


cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / cardiac jelly development / negative regulation of aldosterone biosynthetic process / negative regulation of cortisol biosynthetic process / atrioventricular canal morphogenesis / mesenchymal cell proliferation involved in ureteric bud development / negative regulation of steroid biosynthetic process / embryonic heart tube anterior/posterior pattern specification ...cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / cardiac jelly development / negative regulation of aldosterone biosynthetic process / negative regulation of cortisol biosynthetic process / atrioventricular canal morphogenesis / mesenchymal cell proliferation involved in ureteric bud development / negative regulation of steroid biosynthetic process / embryonic heart tube anterior/posterior pattern specification / positive regulation of extracellular matrix constituent secretion / enzyme activator complex / regulation of odontogenesis of dentin-containing tooth / endodermal-mesodermal cell signaling / negative regulation of cardiac muscle cell differentiation / corticotropin hormone secreting cell differentiation / negative regulation of insulin-like growth factor receptor signaling pathway / thyroid-stimulating hormone-secreting cell differentiation / positive regulation of phosphatase activity / mesenchyme development / ameloblast differentiation / aortic valve development / telencephalon regionalization / negative regulation of collateral sprouting / heart induction / negative regulation of axon regeneration / positive regulation of odontogenesis / positive regulation of cartilage development / positive regulation of peroxisome proliferator activated receptor signaling pathway / Netrin-1 signaling / lung vasculature development / pericardium development / BMP receptor complex / transferrin receptor binding / regulation of BMP signaling pathway / proteoglycan metabolic process / co-receptor binding / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / BMP receptor binding / telencephalon development / positive regulation of odontoblast differentiation / positive regulation of bone mineralization involved in bone maturation / endocardial cushion formation / Transcriptional regulation by RUNX2 / phosphatase activator activity / positive regulation of astrocyte differentiation / cellular response to BMP stimulus / cardiac muscle cell differentiation / Signaling by BMP / astrocyte differentiation / positive regulation of ossification / cardiac muscle tissue morphogenesis / positive regulation of p38MAPK cascade / positive regulation of membrane protein ectodomain proteolysis / atrioventricular valve morphogenesis / endocardial cushion morphogenesis / Molecules associated with elastic fibres / branching involved in ureteric bud morphogenesis / negative regulation of fat cell differentiation / bone mineralization / positive regulation of osteoblast proliferation / odontogenesis of dentin-containing tooth / : / inner ear development / membrane protein ectodomain proteolysis / negative regulation of cell cycle / positive regulation of SMAD protein signal transduction / positive regulation of Wnt signaling pathway / cell fate commitment / epithelial to mesenchymal transition / positive regulation of fat cell differentiation / chondrocyte differentiation / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / positive regulation of epithelial to mesenchymal transition / coreceptor activity / side of membrane / Notch signaling pathway / positive regulation of neuron differentiation / osteoclast differentiation / protein serine/threonine kinase activator activity / animal organ morphogenesis / cytokine activity / skeletal system development / neural tube closure / response to bacterium / growth factor activity / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of canonical Wnt signaling pathway / protein destabilization / bone development / positive regulation of neuron projection development / positive regulation of miRNA transcription / neuron projection development / Regulation of RUNX2 expression and activity / osteoblast differentiation / cell-cell signaling
Similarity search - Function
Repulsive guidance molecule, C-terminal / Repulsive guidance molecule, N-terminal / Repulsive guidance molecule / Repulsive guidance molecule (RGM) C-terminus / Repulsive guidance molecule (RGM) N-terminus / : / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. ...Repulsive guidance molecule, C-terminal / Repulsive guidance molecule, N-terminal / Repulsive guidance molecule / Repulsive guidance molecule (RGM) C-terminus / Repulsive guidance molecule (RGM) N-terminus / : / 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 Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Bone morphogenetic protein 2 / Repulsive guidance molecule A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHealey, E.G. / Bishop, B. / Elegheert, J. / Bell, C.H. / Padilla-Parra, S. / Siebold, C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Repulsive Guidance Molecule is a Structural Bridge between Neogenin and Bone Morphogenetic Protein.
Authors: Healey, E.G. / Bishop, B. / Elegheert, J. / Bell, C.H. / Padilla-Parra, S. / Siebold, C.
History
DepositionMar 27, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Jun 17, 2015Group: Database references
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BONE MORPHOGENETIC PROTEIN 2
B: BONE MORPHOGENETIC PROTEIN 2
C: REPULSIVE GUIDANCE MOLECULE A


Theoretical massNumber of molelcules
Total (without water)37,4773
Polymers37,4773
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-45.6 kcal/mol
Surface area14800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.855, 83.855, 114.843
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.4538, -0.3928, 0.7998), (-0.3842, -0.8961, -0.2221), (0.804, -0.2065, -0.5576)
Vector: 2.887, 84.14, 35.38)

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Components

#1: Protein BONE MORPHOGENETIC PROTEIN 2 / BMP-2 / BONE MORPHOGENETIC PROTEIN 2A / BMP-2A / BONE MORPHOGENETIC PROTEIN 2 / BMP2


Mass: 12923.854 Da / Num. of mol.: 2
Fragment: C-TERMINAL DOMAIN SIGNALING DOMAIN, RESIDUES 283-396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: P12643
#2: Protein REPULSIVE GUIDANCE MOLECULE A / RGM DOMAIN FAMILY MEMBER A / RGMA


Mass: 11628.836 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 45-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q96B86
Has protein modificationY
Sequence detailsN-TERMINAL DOMAIN OF HUMAN RGMA WITH 3 ADDITIONAL N- TERMINAL RESIDUES (ETG) AND 9 ADDITIONAL C- ...N-TERMINAL DOMAIN OF HUMAN RGMA WITH 3 ADDITIONAL N- TERMINAL RESIDUES (ETG) AND 9 ADDITIONAL C-TERMINAL RESIDUES (GTKHHHHHH).

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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: 3.12 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 4
Details: 0.1 M CITRIC ACID, PH 4.0, 20% (V/V) 2-METHYL-2,4-PENTANEDIOL (MPD), 0.2 M GLYCINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.0163
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0163 Å / Relative weight: 1
ReflectionResolution: 3.2→45 Å / Num. obs: 8086 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 78.56 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.1
Reflection shellResolution: 3.2→3.42 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→45.04 Å / Cor.coef. Fo:Fc: 0.8219 / Cor.coef. Fo:Fc free: 0.7773 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.428
RfactorNum. reflection% reflectionSelection details
Rfree0.264 372 4.61 %RANDOM
Rwork0.2271 ---
obs0.2287 8074 99.85 %-
Displacement parametersBiso mean: 110.08 Å2
Baniso -1Baniso -2Baniso -3
1--31.9331 Å20 Å20 Å2
2---31.9331 Å20 Å2
3---63.8662 Å2
Refine analyzeLuzzati coordinate error obs: 0.8 Å
Refinement stepCycle: LAST / Resolution: 3.2→45.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2112 0 0 0 2112
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012176HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.152967HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d971SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes50HARMONIC2
X-RAY DIFFRACTIONt_gen_planes315HARMONIC5
X-RAY DIFFRACTIONt_it2176HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion3.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion279SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2534SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.58 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2542 90 4.01 %
Rwork0.2324 2156 -
all0.2331 2246 -
obs--99.85 %

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