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- PDB-6z3h: Repulsive Guidance Molecule B (RGMB) in complex with Growth Diffe... -

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Basic information

Entry
Database: PDB / ID: 6z3h
TitleRepulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) (crystal form 2)
Components
  • Growth/differentiation factor 5
  • RGM domain family member B
KeywordsSIGNALING PROTEIN / Repulsive Guidance Molecule / RGM / Bone Morphogenetic Protein / BMP / Growth Differentiation Factor 5 / GDF5 / Neogenin / axon guidance / TGFbeta signalling / brain development / iron metabolism.
Function / homology
Function and homology information


ossification involved in bone remodeling / forelimb morphogenesis / chondroblast differentiation / BMP binding / hindlimb morphogenesis / negative regulation of mesenchymal cell apoptotic process / Netrin-1 signaling / positive regulation of chondrocyte differentiation / mesenchymal cell apoptotic process / positive regulation of BMP signaling pathway ...ossification involved in bone remodeling / forelimb morphogenesis / chondroblast differentiation / BMP binding / hindlimb morphogenesis / negative regulation of mesenchymal cell apoptotic process / Netrin-1 signaling / positive regulation of chondrocyte differentiation / mesenchymal cell apoptotic process / positive regulation of BMP signaling pathway / negative regulation of chondrocyte differentiation / embryonic limb morphogenesis / Molecules associated with elastic fibres / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of SMAD protein signal transduction / regulation of multicellular organism growth / chondrocyte differentiation / response to mechanical stimulus / BMP signaling pathway / coreceptor activity / side of membrane / positive regulation of neuron differentiation / transforming growth factor beta receptor signaling pathway / cytokine activity / growth factor activity / negative regulation of epithelial cell proliferation / cell-cell signaling / negative regulation of neuron apoptotic process / cell adhesion / membrane raft / positive regulation of DNA-templated transcription / signal transduction / extracellular space / extracellular region / identical protein binding / plasma membrane
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. / Transforming growth factor-beta-related ...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 cytokine
Similarity search - Domain/homology
Growth/differentiation factor 5 / Repulsive guidance molecule B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.158 Å
AuthorsMalinauskas, T. / Peer, T.V. / Bishop, B. / Muller, T.D. / Siebold, C.
Funding support United Kingdom, Germany, 7items
OrganizationGrant numberCountry
Cancer Research UKC20724/A14414 United Kingdom
Cancer Research UKC20724/A26752 United Kingdom
European Research Council (ERC)647278 United Kingdom
German Research Foundation (DFG)MU1095/3-2 Germany
German Research Foundation (DFG)MU1095/5-1 Germany
Wellcome Trust203852/Z/16/2 United Kingdom
Human Frontier Science Program (HFSP)LT000021/2014-L United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Repulsive guidance molecules lock growth differentiation factor 5 in an inhibitory complex.
Authors: Malinauskas, T. / Peer, T.V. / Bishop, B. / Mueller, T.D. / Siebold, C.
History
DepositionMay 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Growth/differentiation factor 5
B: RGM domain family member B


Theoretical massNumber of molelcules
Total (without water)23,9382
Polymers23,9382
Non-polymers00
Water00
1
A: Growth/differentiation factor 5
B: RGM domain family member B

A: Growth/differentiation factor 5
B: RGM domain family member B


Theoretical massNumber of molelcules
Total (without water)47,8764
Polymers47,8764
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/31
Buried area6450 Å2
ΔGint-58 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.860, 98.860, 99.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Growth/differentiation factor 5 / GDF-5 / Bone morphogenetic protein 14 / BMP-14 / Cartilage-derived morphogenetic protein 1 / CDMP-1 ...GDF-5 / Bone morphogenetic protein 14 / BMP-14 / Cartilage-derived morphogenetic protein 1 / CDMP-1 / Lipopolysaccharide-associated protein 4 / LPS-associated protein 4 / Radotermin


Mass: 13405.481 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GDF5, BMP14, CDMP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P43026
#2: Protein RGM domain family member B / DRG11-responsive axonal guidance and outgrowth of neurite / DRAGON


Mass: 10532.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RGMB / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q6NW40
Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M (NH4)2SO4, 0.1 M sodium acetate pH 4.6, 35% w/v pentaerythritol ethoxylate (15/4 EO/OH; average MW 797 Da)
PH range: 4.6-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.13→64.98 Å / Num. obs: 5352 / % possible obs: 97.6 % / Redundancy: 35.8 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 23.4
Reflection shellResolution: 3.13→3.21 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 380 / CC1/2: 0.806

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Processing

Software
NameVersionClassification
PHENIX(1.15rc3_3435: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UI0

4ui0


Resolution: 3.158→49.43 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2682 191 4.44 %
Rwork0.2345 --
obs0.2362 4299 80.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.158→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 0 0 0 1230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011254
X-RAY DIFFRACTIONf_angle_d0.3761703
X-RAY DIFFRACTIONf_dihedral_angle_d9.344761
X-RAY DIFFRACTIONf_chiral_restr0.036196
X-RAY DIFFRACTIONf_plane_restr0.004220
LS refinement shellResolution: 3.158→49.43 Å
RfactorNum. reflection% reflection
Rfree0.2682 191 -
Rwork0.2345 4108 -
obs--81 %
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)
11.13030.1164-0.04222.4870.15321.22310.26560.32450.405-0.1248-0.1593-1.3713-0.5011.1006-1.41020.2228-0.4515-0.01760.83830.11460.8005-44.573825.79289.6914
29.53170.53993.20750.21371.32848.1951.6430.4495-0.26811.4479-0.2907-2.6241-0.12691.3532-1.31261.3846-0.4648-0.45961.82670.26872.7907-31.55610.771421.4228
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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