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- PDB-4ui0: Crystal structure of the human RGMB-BMP2 complex, crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 4ui0
TitleCrystal structure of the human RGMB-BMP2 complex, crystal form 2
Components
  • BONE MORPHOGENETIC PROTEIN 2
  • RGM DOMAIN FAMILY MEMBER B
KeywordsSIGNALING PROTEIN / REPULSIVE GUIDANCE MOLECULE / 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 / corticotropin hormone secreting cell differentiation / thyroid-stimulating hormone-secreting cell differentiation / cardiac jelly development / negative regulation of steroid biosynthetic process / negative regulation of aldosterone biosynthetic process / negative regulation of cortisol biosynthetic process / embryonic heart tube anterior/posterior pattern specification ...cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / corticotropin hormone secreting cell differentiation / thyroid-stimulating hormone-secreting cell differentiation / cardiac jelly development / negative regulation of steroid biosynthetic process / negative regulation of aldosterone biosynthetic process / negative regulation of cortisol biosynthetic process / embryonic heart tube anterior/posterior pattern specification / positive regulation of extracellular matrix constituent secretion / atrioventricular canal morphogenesis / pericardium development / mesenchymal cell proliferation involved in ureteric bud development / telencephalon regionalization / negative regulation of cardiac muscle cell differentiation / negative regulation of insulin-like growth factor receptor signaling pathway / positive regulation of odontogenesis / endodermal-mesodermal cell signaling / positive regulation of phosphatase activity / aortic valve development / positive regulation of cartilage development / heart induction / lung vasculature development / Netrin-1 signaling / positive regulation of peroxisome proliferator activated receptor signaling pathway / mesenchyme development / BMP receptor complex / positive regulation of astrocyte differentiation / co-receptor binding / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / positive regulation of bone mineralization involved in bone maturation / positive regulation of odontoblast differentiation / telencephalon development / Transcriptional regulation by RUNX2 / BMP receptor binding / phosphatase activator activity / endocardial cushion formation / cellular response to BMP stimulus / cardiac muscle cell differentiation / cardiac muscle tissue morphogenesis / Signaling by BMP / odontogenesis of dentin-containing tooth / positive regulation of ossification / branching involved in ureteric bud morphogenesis / positive regulation of p38MAPK cascade / atrioventricular valve morphogenesis / negative regulation of fat cell differentiation / endocardial cushion morphogenesis / Molecules associated with elastic fibres / positive regulation of osteoblast proliferation / inner ear development / positive regulation of bone mineralization / bone mineralization / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of cell cycle / chondrocyte differentiation / positive regulation of SMAD protein signal transduction / cell fate commitment / heart morphogenesis / epithelial to mesenchymal transition / BMP signaling pathway / positive regulation of fat cell differentiation / Notch signaling pathway / positive regulation of epithelial to mesenchymal transition / positive regulation of Wnt signaling pathway / osteoclast differentiation / side of membrane / coreceptor activity / skeletal system development / positive regulation of neuron differentiation / animal organ morphogenesis / cytokine activity / 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 / in utero embryonic development / bone development / positive regulation of miRNA transcription / positive regulation of protein phosphorylation / gene expression / osteoblast differentiation / heart development / Regulation of RUNX2 expression and activity / cell-cell signaling / intracellular iron ion homeostasis / response to hypoxia / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / cell adhesion / positive regulation of cell migration / positive regulation of apoptotic process / inflammatory response / membrane raft / negative regulation of cell population proliferation / negative regulation of gene expression / signaling receptor binding / negative regulation of DNA-templated transcription
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 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
CITRATE ANION / Bone morphogenetic protein 2 / Repulsive guidance molecule B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.3Oct 23, 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: BONE MORPHOGENETIC PROTEIN 2
C: RGM DOMAIN FAMILY MEMBER B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7236
Polymers36,3803
Non-polymers3433
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-49.5 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.021, 85.021, 115.182
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: (0.4466, -0.4321, 0.7835), (-0.4297, -0.8716, -0.2358), (0.7848, -0.2314, -0.575)
Vector: -3.306, -34.94, -13.23)

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Components

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Protein , 2 types, 3 molecules ABC

#1: Protein BONE MORPHOGENETIC PROTEIN 2 / BMP-2 / BONE MORPHOGENETIC PROTEIN 2A / BMP-2A / 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 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 53-136
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

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Non-polymers , 4 types, 23 molecules

#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.3 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growpH: 4 / Details: 0.08 M CITRIC ACID PH 4.0, 15% (V/V) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.8→45 Å / Num. obs: 13647 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Biso Wilson estimate: 69.81 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.7 / % possible all: 99.4

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→45 Å / Cor.coef. Fo:Fc: 0.8968 / Cor.coef. Fo:Fc free: 0.9102 / SU R Cruickshank DPI: 0.462 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.473 / SU Rfree Blow DPI: 0.303 / SU Rfree Cruickshank DPI: 0.304
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2665 588 4.79 %RANDOM
Rwork0.2327 ---
obs0.2344 12284 99.85 %-
Displacement parametersBiso mean: 87.99 Å2
Baniso -1Baniso -2Baniso -3
1--12.7622 Å20 Å20 Å2
2---12.7622 Å20 Å2
3---25.5243 Å2
Refine analyzeLuzzati coordinate error obs: 0.546 Å
Refinement stepCycle: LAST / Resolution: 2.8→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 22 20 2060
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012094HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.082854HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d939SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes49HARMONIC2
X-RAY DIFFRACTIONt_gen_planes301HARMONIC5
X-RAY DIFFRACTIONt_it2094HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion3.05
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion269SEMIHARMONIC5
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_contact2371SEMIHARMONIC4
LS refinement shellResolution: 2.8→3.07 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4208 142 4.92 %
Rwork0.3448 2742 -
all0.3482 2884 -
obs--99.85 %
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)
12.62051.7185-2.31561.1108-1.17954.50050.02690.01420.1531-0.04990.04950.1648-0.2026-0.1697-0.0764-0.00660.13630.0108-0.0095-0.0417-0.212535.9843-34.349423.2569
23.71492.1684-3.6762.9764-3.43945.5895-0.2133-0.00760.1702-0.15480.14030.1379-0.1878-0.22060.07290.12870.1186-0.0202-0.1312-0.0676-0.296245.6479-26.53579.74
31.4332-0.1409-2.0015.05174.90684.1167-0.08730.3845-0.0091-0.30540.18650.1450.2127-0.0811-0.09920.31870.03840.19130.0481-0.1309-0.358134.6028-54.396912.3319
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|293 - A|396 }
2X-RAY DIFFRACTION2{ B|293 - B|396 }
3X-RAY DIFFRACTION3{ C|53 - C|121 }

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