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- PDB-4ui2: Crystal structure of the ternary RGMB-BMP2-NEO1 complex -

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Basic information

Entry
Database: PDB / ID: 4ui2
TitleCrystal structure of the ternary RGMB-BMP2-NEO1 complex
Components
  • (REPULSIVE GUIDANCE MOLECULE C, RGMC, ...) x 2
  • BONE MORPHOGENETIC PROTEIN 2, BMP2
  • NEOGENINNEO1
KeywordsSIGNALING PROTEIN / REPULSIVE GUIDANCE MOLECULE / BONE MORPHOGENETIC PROTEIN PATHWAY / HEMOJUVELIN / MORPHOGEN / AXON GUIDANCE / CELL SURFACE RECEPTOR SIGNALING / NEOGENIN
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 / positive regulation of odontogenesis / regulation of odontogenesis of dentin-containing tooth / endodermal-mesodermal cell signaling / corticotropin hormone secreting cell differentiation / lung vasculature development / negative regulation of insulin-like growth factor receptor signaling pathway / thyroid-stimulating hormone-secreting cell differentiation / mesenchyme development / aortic valve development / telencephalon regionalization / positive regulation of phosphatase activity / positive regulation of cartilage development / proteoglycan metabolic process / heart induction / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of axon regeneration / Netrin-1 signaling / pericardium development / BMP receptor complex / co-receptor binding / telencephalon development / cardiac epithelial to mesenchymal transition / BMP receptor binding / mesenchymal cell differentiation / positive regulation of odontoblast differentiation / endocardial cushion formation / positive regulation of bone mineralization involved in bone maturation / Transcriptional regulation by RUNX2 / phosphatase activator activity / regulation of axon regeneration / positive regulation of astrocyte differentiation / Signaling by BMP / cardiac muscle cell differentiation / cellular response to BMP stimulus / myoblast fusion / cardiac muscle tissue morphogenesis / plasma membrane protein complex / positive regulation of BMP signaling pathway / positive regulation of ossification / astrocyte differentiation / Molecules associated with elastic fibres / atrioventricular valve morphogenesis / positive regulation of p38MAPK cascade / endocardial cushion morphogenesis / negative regulation of fat cell differentiation / branching involved in ureteric bud morphogenesis / intracellular vesicle / Myogenesis / bone mineralization / odontogenesis of dentin-containing tooth / positive regulation of osteoblast proliferation / inner ear development / positive regulation of SMAD protein signal transduction / protein secretion / positive regulation of Wnt signaling pathway / cellular response to organic cyclic compound / negative regulation of cell cycle / endoplasmic reticulum-Golgi intermediate compartment / epithelial to mesenchymal transition / positive regulation of epithelial to mesenchymal transition / positive regulation of fat cell differentiation / positive regulation of osteoblast differentiation / cell fate commitment / negative regulation of protein secretion / chondrocyte differentiation / BMP signaling pathway / positive regulation of bone mineralization / coreceptor activity / side of membrane / axonal growth cone / 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 / axon guidance / negative regulation of smooth muscle cell proliferation / response to bacterium / animal organ morphogenesis / negative regulation of transforming growth factor beta receptor signaling pathway / neuron migration / growth factor activity / protein destabilization / bone development / negative regulation of canonical Wnt signaling pathway
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 / Mog1/PsbP, alpha/beta/alpha sandwich / : / Protein Transport Mog1p; Chain A / Neogenin, C-terminal / Neogenin C-terminus ...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 / Mog1/PsbP, alpha/beta/alpha sandwich / : / Protein Transport Mog1p; Chain A / Neogenin, C-terminal / Neogenin C-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 / Immunoglobulin domain / Cystine-knot cytokine / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Ribbon / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / S,R MESO-TARTARIC ACID / Bone morphogenetic protein 2 / Neogenin / Repulsive guidance molecule B / Neogenin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 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 1.3Jun 20, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEOGENIN
B: BONE MORPHOGENETIC PROTEIN 2, BMP2
C: REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN
D: REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5069
Polymers83,4104
Non-polymers1,0965
Water0
1
A: NEOGENIN
B: BONE MORPHOGENETIC PROTEIN 2, BMP2
C: REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN
D: REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN
hetero molecules

A: NEOGENIN
B: BONE MORPHOGENETIC PROTEIN 2, BMP2
C: REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN
D: REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,01118
Polymers166,8198
Non-polymers2,19210
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area19580 Å2
ΔGint-82.8 kcal/mol
Surface area52290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.080, 120.080, 204.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein NEOGENIN / NEO1


Mass: 29221.842 Da / Num. of mol.: 1 / Fragment: 5TH AND 6TH FN TYPE 3 LIKE DOMAINS
Source method: isolated from a genetically manipulated source
Details: CHAIN C AND CHAIN D IS THE RESULT OF AN AUTOCATALYTIC CLEAVAGE BETWEEN RESIDUES ASP168 AND PRO169
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: P97798, UniProt: Q92859*PLUS
#2: Protein BONE MORPHOGENETIC PROTEIN 2, BMP2


Mass: 12923.854 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN SIGNALING DOMAIN
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

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REPULSIVE GUIDANCE MOLECULE C, RGMC, ... , 2 types, 2 molecules CD

#3: Protein REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN


Mass: 13318.698 Da / Num. of mol.: 1 / Fragment: RESIDUES 50-168
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
#4: Protein REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN


Mass: 27945.352 Da / Num. of mol.: 1 / Fragment: RESIDUES 169-240
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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Sugars , 1 types, 1 molecules

#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 4 molecules

#6: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#7: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2

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Details

Nonpolymer detailsBETA-D-MANNOSE (BMA): BELONGS TO THE N-LINKED GLYCOSYLATION SITE, COVALENTLY BOUND TO NAG D 1195 N- ...BETA-D-MANNOSE (BMA): BELONGS TO THE N-LINKED GLYCOSYLATION SITE, COVALENTLY BOUND TO NAG D 1195 N-ACETYL-D-GLUCOSAMINE (NAG): BELONG TO THE N-LINKED GLYCOSYLATION SITE. NAG D 1193 IS COVALENTLY LINKED TO ASN A 940
Sequence detailsECTODOMAIN OF HUMAN RGMB WITH 3 ADDITIONAL N-TERMINAL RESIDUES (ETG) AND 9 ADDITIONAL C-TERMINAL ...ECTODOMAIN OF HUMAN RGMB WITH 3 ADDITIONAL N-TERMINAL RESIDUES (ETG) AND 9 ADDITIONAL C-TERMINAL RESIDUES ( GTKHHHHHH). 5TH AND 6TH FN TYPE 3 LIKE DOMAINS OF MOUSE NEO1 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: 4.43 Å3/Da / Density % sol: 72 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M TRIS-HCL PH 8.5, 1.5 M AMMONIUM SULPHATE, 12% (V/V) GLYCEROL

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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 / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.15→103.5 Å / Num. obs: 26245 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.2
Reflection shellResolution: 3.15→3.23 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 1.5 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→50.01 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 42.631 / SU ML: 0.295 / Cross valid method: THROUGHOUT / ESU R: 0.472 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. THE DISULPHIDE LINKED BMP2 DIMER IS ON A TWO-FOLD CRYSTALLOGRAPHIC AXIS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23609 1248 4.8 %RANDOM
Rwork0.19591 ---
obs0.19779 24934 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 133.545 Å2
Baniso -1Baniso -2Baniso -3
1-5.46 Å20 Å20 Å2
2--5.46 Å20 Å2
3----10.92 Å2
Refinement stepCycle: LAST / Resolution: 3.15→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4238 0 73 0 4311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194420
X-RAY DIFFRACTIONr_bond_other_d0.0020.024079
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.966016
X-RAY DIFFRACTIONr_angle_other_deg1.12739414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9825534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20923.947190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6515707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2871524
X-RAY DIFFRACTIONr_chiral_restr0.1020.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214919
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02995
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5278.572158
X-RAY DIFFRACTIONr_mcbond_other4.5178.5642156
X-RAY DIFFRACTIONr_mcangle_it7.39812.8272684
X-RAY DIFFRACTIONr_mcangle_other7.39912.8322685
X-RAY DIFFRACTIONr_scbond_it5.2749.3762261
X-RAY DIFFRACTIONr_scbond_other5.2729.3772262
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.48613.8523333
X-RAY DIFFRACTIONr_long_range_B_refined13.42982.32817939
X-RAY DIFFRACTIONr_long_range_B_other13.42882.3317940
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.15→3.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 81 -
Rwork0.41 1751 -
obs--96.12 %
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)
15.0581-2.04062.21923.0011-4.42296.7419-0.0710.6959-0.5309-0.1714-0.1617-0.03580.186-0.02660.23280.91240.1116-0.10580.4352-0.24190.168741.9123.447-26.166
21.2759-0.9571.65352.16430.46884.29750.3080.16620.03030.30290.0096-0.2481.40420.4348-0.31761.14410.4001-0.18650.43850.01560.068660.099-17.7187.518
36.05592.8843.98412.99762.80783.171-0.13540.37470.1586-0.34050.10590.1088-0.31360.15780.02950.52250.00310.0790.37420.09030.223731.822-19.759-48.184
40.46540.7013-0.05871.43710.88382.53190.3515-0.26040.28240.4411-0.65460.559-0.1223-0.63670.30310.8906-0.00550.24030.76010.10680.595924.817-22.889-25.625
50.7672-0.59090.38931.38280.53893.42340.0658-0.2264-0.0076-0.0402-0.10270.15880.5668-0.09620.03690.5028-0.00320.00150.50740.04590.120346.177-0.34610.745
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A883 - 982
2X-RAY DIFFRACTION2A983 - 1085
3X-RAY DIFFRACTION3B293 - 396
4X-RAY DIFFRACTION4C52 - 122
5X-RAY DIFFRACTION5C137 - 323

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