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- PDB-4ui1: Crystal structure of the human RGMC-BMP2 complex -

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Basic information

Entry
Database: PDB / ID: 4ui1
TitleCrystal structure of the human RGMC-BMP2 complex
Components
  • BONE MORPHOGENETIC PROTEIN 2
  • HEMOJUVELIN
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 / embryonic heart tube anterior/posterior pattern specification / atrioventricular canal morphogenesis / negative regulation of cortisol biosynthetic process / mesenchymal cell proliferation involved in ureteric bud development / negative regulation of steroid biosynthetic process ...cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / cardiac jelly development / negative regulation of aldosterone biosynthetic process / embryonic heart tube anterior/posterior pattern specification / atrioventricular canal morphogenesis / negative regulation of cortisol biosynthetic process / mesenchymal cell proliferation involved in ureteric bud development / negative regulation of steroid biosynthetic process / ameloblast differentiation / positive regulation of extracellular matrix constituent secretion / negative regulation of cardiac muscle cell differentiation / regulation of odontogenesis of dentin-containing tooth / endodermal-mesodermal cell signaling / corticotropin hormone secreting cell differentiation / negative regulation of insulin-like growth factor receptor signaling pathway / thyroid-stimulating hormone-secreting cell differentiation / mesenchyme development / aortic valve development / BMP binding / telencephalon regionalization / positive regulation of phosphatase activity / positive regulation of odontogenesis / positive regulation of cartilage development / proteoglycan metabolic process / heart induction / positive regulation of peroxisome proliferator activated receptor signaling pathway / Netrin-1 signaling / pericardium development / lung vasculature development / BMP receptor complex / co-receptor binding / transferrin receptor binding / telencephalon development / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / BMP receptor binding / positive regulation of odontoblast differentiation / endocardial cushion formation / positive regulation of bone mineralization involved in bone maturation / phosphatase activator activity / Transcriptional regulation by RUNX2 / positive regulation of astrocyte differentiation / Signaling by BMP / cellular response to BMP stimulus / cardiac muscle cell differentiation / activin receptor signaling pathway / cardiac muscle tissue morphogenesis / plasma membrane protein complex / positive regulation of ossification / astrocyte differentiation / Molecules associated with elastic fibres / atrioventricular valve morphogenesis / positive regulation of p38MAPK cascade / endocardial cushion morphogenesis / branching involved in ureteric bud morphogenesis / negative regulation of fat cell differentiation / bone mineralization / positive regulation of osteoblast proliferation / odontogenesis of dentin-containing tooth / positive regulation of SMAD protein signal transduction / inner ear development / protein autoprocessing / cellular response to organic cyclic compound / negative regulation of BMP signaling pathway / negative regulation of cell cycle / positive regulation of Wnt signaling pathway / positive regulation of fat cell differentiation / epithelial to mesenchymal transition / cell fate commitment / chondrocyte differentiation / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / coreceptor activity / side of membrane / positive regulation of epithelial to mesenchymal transition / Notch signaling pathway / positive regulation of neuron differentiation / protein serine/threonine kinase activator activity / osteoclast differentiation / negative regulation of MAP kinase activity / skeletal system development / cytokine activity / negative regulation of smooth muscle cell proliferation / animal organ morphogenesis / negative regulation of transforming growth factor beta receptor signaling pathway / response to bacterium / growth factor activity / protein destabilization / bone development / negative regulation of canonical Wnt signaling pathway / HFE-transferrin receptor complex / multicellular organismal-level iron ion homeostasis / positive regulation of DNA-binding transcription factor activity / positive regulation of miRNA transcription / osteoblast differentiation / Regulation of RUNX2 expression and activity / positive regulation of protein binding
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
NITRATE ION / Bone morphogenetic protein 2 / Hemojuvelin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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

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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: HEMOJUVELIN
D: HEMOJUVELIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,34115
Polymers50,7124
Non-polymers62911
Water1,53185
1
A: BONE MORPHOGENETIC PROTEIN 2
D: HEMOJUVELIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6137
Polymers25,3562
Non-polymers2575
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-21 kcal/mol
Surface area12050 Å2
MethodPISA
2
B: BONE MORPHOGENETIC PROTEIN 2
C: HEMOJUVELIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7288
Polymers25,3562
Non-polymers3726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-12.8 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.040, 76.290, 81.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9217, -0.3868, 0.02956), (-0.3868, 0.9106, -0.1457), (0.02945, -0.1458, -0.9889)61.4, 14.35, 25.65
2given(-0.9318, -0.3579, 0.06109), (-0.3631, 0.9169, -0.166), (0.003403, -0.1769, -0.9842)60.56, 14.24, 26.83

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Components

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Protein , 2 types, 4 molecules ABCD

#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 HEMOJUVELIN / / HEMOCHROMATOSIS TYPE 2 PROTEIN / RGM DOMAIN FAMILY MEMBER C / REPULSIVE GUIDANCE MOLECULE C / RGMC


Mass: 12432.020 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 35-145
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: Q6ZVN8

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Non-polymers , 4 types, 96 molecules

#3: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsN-TERMINAL DOMAIN OF HUMAN RGMC WITH 3 ADDITIONAL N- TERMINAL RESIDUES (ETG) AND 9 ADDITIONAL C- ...N-TERMINAL DOMAIN OF HUMAN RGMC 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: 2.13 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 7.5 / Details: 20% (W/V) PEG3350, 0.2 M AMMONIUM NITRATE, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 18558 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 40.32 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.7
Reflection shellResolution: 2.35→2.45 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→43.38 Å / Cor.coef. Fo:Fc: 0.9191 / Cor.coef. Fo:Fc free: 0.8894 / SU R Cruickshank DPI: 0.286 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.3 / SU Rfree Blow DPI: 0.224 / SU Rfree Cruickshank DPI: 0.222
RfactorNum. reflection% reflectionSelection details
Rfree0.238 918 5.06 %RANDOM
Rwork0.1865 ---
obs0.189 18135 97.64 %-
Displacement parametersBiso mean: 54.76 Å2
Baniso -1Baniso -2Baniso -3
1-9.8881 Å20 Å20 Å2
2---22.3994 Å20 Å2
3---12.5113 Å2
Refine analyzeLuzzati coordinate error obs: 0.318 Å
Refinement stepCycle: LAST / Resolution: 2.35→43.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2730 0 38 85 2853
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012833HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.093841HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1278SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes416HARMONIC5
X-RAY DIFFRACTIONt_it2833HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.12
X-RAY DIFFRACTIONt_other_torsion3.03
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion363SEMIHARMONIC5
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_contact3312SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.49 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.245 131 4.99 %
Rwork0.2081 2495 -
all0.2099 2626 -
obs--97.64 %
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)
12.20741.14811.7670.93291.92154.68590.1402-0.1420.13180.046-0.21120.1017-0.0362-0.48290.071-0.1024-0.049-0.02260.0695-0.0024-0.126121.59719.09519.0283
23.7510.42073.01030.23821.13145.1330.04020.17650.0067-0.07780.06090.0342-0.14310.2942-0.1011-0.0895-0.08920.00230.0457-0.0142-0.141938.182313.259615.8404
32.1187-0.4167-0.01874.1146-1.99996.5259-0.05460.31350.0272-0.2545-0.3459-0.3797-0.33750.29280.4005-0.1321-0.0179-0.05080.15460.0485-0.201828.579513.541-14.4657
43.9228-1.4456-0.6784.10831.06723.77330.113-0.77360.00690.2763-0.1990.04840.1434-0.33870.086-0.1935-0.14030.02790.3186-0.0978-0.271129.83519.04639.5613
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|293 - A|396 }
2X-RAY DIFFRACTION2{ B|292 - B|396 }
3X-RAY DIFFRACTION3{ C|35 - C|128 }
4X-RAY DIFFRACTION4{ D|36 - D|129 }

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