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- PDB-4uhz: Crystal structure of the human RGMB-BMP2 complex, crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 4uhz
TitleCrystal structure of the human RGMB-BMP2 complex, crystal form 1
Components
  • BONE MORPHOGENETIC PROTEIN 2
  • RGM DOMAIN FAMILY MEMBER B
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 / positive regulation of phosphatase activity / cardiac jelly development / positive regulation of extracellular matrix constituent secretion / negative regulation of aldosterone biosynthetic process / negative regulation of cortisol biosynthetic process / atrioventricular canal morphogenesis / mesenchymal cell proliferation involved in ureteric bud development ...cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / positive regulation of phosphatase activity / cardiac jelly development / positive regulation of extracellular matrix constituent secretion / 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 / 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 / thyroid-stimulating hormone-secreting cell differentiation / mesenchyme development / ameloblast differentiation / negative regulation of insulin-like growth factor receptor signaling pathway / aortic valve development / pericardium development / telencephalon regionalization / heart induction / positive regulation of cartilage development / positive regulation of odontogenesis / Netrin-1 signaling / positive regulation of peroxisome proliferator activated receptor signaling pathway / BMP receptor complex / proteoglycan metabolic process / co-receptor binding / lung vasculature development / 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 / Signaling by BMP / cardiac muscle cell differentiation / astrocyte differentiation / cardiac muscle tissue morphogenesis / positive regulation of ossification / positive regulation of p38MAPK cascade / atrioventricular valve morphogenesis / endocardial cushion morphogenesis / Molecules associated with elastic fibres / branching involved in ureteric bud morphogenesis / positive regulation of osteoblast proliferation / negative regulation of fat cell differentiation / bone mineralization / endoplasmic reticulum-Golgi intermediate compartment / odontogenesis of dentin-containing tooth / inner ear development / negative regulation of cell cycle / positive regulation of SMAD protein signal transduction / epithelial to mesenchymal transition / cell fate commitment / positive regulation of Wnt signaling pathway / 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 / response to bacterium / negative regulation of smooth muscle cell proliferation / growth factor activity / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of canonical Wnt signaling pathway / protein destabilization / bone development / positive regulation of miRNA transcription / Regulation of RUNX2 expression and activity / positive regulation of protein phosphorylation / osteoblast differentiation / cell-cell signaling / heart development / in utero embryonic development / transcription by RNA polymerase II / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / cell adhesion / positive regulation of MAPK cascade / cilium
Similarity search - Function
Repulsive guidance molecule, C-terminal / Repulsive guidance molecule, N-terminal / Repulsive guidance molecule / Repulsive guidance molecule (RGM) C-terminal domain / Repulsive guidance molecule (RGM) N-terminal domain / : / 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-terminal domain / Repulsive guidance molecule (RGM) N-terminal domain / : / 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 B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: RGM DOMAIN FAMILY MEMBER B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,22510
Polymers23,4572
Non-polymers7698
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-91.5 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.010, 129.010, 129.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

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


Mass: 12923.854 Da / Num. of mol.: 1
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 RGM DOMAIN FAMILY MEMBER B / DRG11-RESPONSIVE AXONAL GUIDANCE AND OUTGROWTH OF NEURITE / DRAGON / REPULSIVE GUIDANCE MOLECULE B / RGMB


Mass: 10532.701 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 52-137
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: Q6NW40
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY
Sequence detailsN-TERMINAL DOMAIN OF HUMAN RGMB WITH 3 ADDITIONAL N- TERMINAL RESIDUES (ETG) AND 9 ADDITIONAL C- ...N-TERMINAL DOMAIN OF HUMAN RGMB 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: 3.82 Å3/Da / Density % sol: 68 % / Description: NONE
Crystal growDetails: 2 M AMMONIUM SULPHATE, 8% (V/V) 2,5- HEXANEDIOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 8429 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 117.52 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.1
Reflection shellResolution: 2.85→2.93 Å / Redundancy: 4 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.5 / % possible all: 98.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→50 Å / Cor.coef. Fo:Fc: 0.9418 / Cor.coef. Fo:Fc free: 0.9384 / SU R Cruickshank DPI: 0.402 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.399 / SU Rfree Blow DPI: 0.26 / SU Rfree Cruickshank DPI: 0.263
Details: DEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 390 4.63 %RANDOM
Rwork0.205 ---
obs0.206 8427 99.22 %-
Displacement parametersBiso mean: 112.03 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.561 Å
Refinement stepCycle: LAST / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1345 0 40 0 1385
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091413HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.031925HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d630SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes33HARMONIC2
X-RAY DIFFRACTIONt_gen_planes201HARMONIC5
X-RAY DIFFRACTIONt_it1413HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.33
X-RAY DIFFRACTIONt_other_torsion3.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion178SEMIHARMONIC5
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_contact1523SEMIHARMONIC4
LS refinement shellResolution: 2.85→3.19 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2795 96 4.09 %
Rwork0.2351 2251 -
all0.237 2347 -
obs--99.22 %
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)
16.7760.1957-0.57111.3787-0.09481.60420.0282-0.26940.0991-0.0867-0.08890.14440.032-0.10960.06070.00130.0176-0.0322-0.0977-0.0425-0.2316152.38615.9772131.19
22.4791-1.7374-2.56622.1008-2.19569.43680.03050.41030.4784-0.1811-0.0011-0.00620.0069-0.0544-0.0294-0.20980.0198-0.16770.3193-0.0121-0.3517148.12320.2045107.862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|293 - A|396 }
2X-RAY DIFFRACTION2{ B|53 - B|122 }

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