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- PDB-6z3j: Repulsive Guidance Molecule B (RGMB) in complex with Growth Diffe... -

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Basic information

Entry
Database: PDB / ID: 6z3j
TitleRepulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) (crystal form 1)
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 / BMP binding / chondroblast differentiation / 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 / BMP binding / chondroblast differentiation / 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 / BMP signaling pathway / chondrocyte differentiation / response to mechanical stimulus / 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-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 ...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 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: 1.65 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: Growth/differentiation factor 5
C: RGM domain family member B
D: RGM domain family member B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,67215
Polymers47,7824
Non-polymers89011
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, light scattering, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-96 kcal/mol
Surface area17790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.480, 127.750, 39.910
Angle α, β, γ (deg.)90.00, 99.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ABCD

#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: 13358.446 Da / Num. of mol.: 2 / Mutation: Y487K, Q489D
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.: 2
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

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Sugars , 1 types, 1 molecules

#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 152 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 1.92 Å3/Da / Density % sol: 35.96 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.2 M Li2SO4, 0.1 M HEPES pH 7.5, 25% v/v PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.65→39.38 Å / Num. obs: 43071 / % possible obs: 99.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 9.5
Reflection shellResolution: 1.65→1.69 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3117 / CC1/2: 0.212

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Processing

Software
NameVersionClassification
PHENIX(1.13rc2_2986: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z3H

6z3h


Resolution: 1.65→39.38 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2193 2173 5.07 %
Rwork0.1906 --
obs0.1921 42900 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→39.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2804 0 51 142 2997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052936
X-RAY DIFFRACTIONf_angle_d0.8553979
X-RAY DIFFRACTIONf_dihedral_angle_d12.3461820
X-RAY DIFFRACTIONf_chiral_restr0.047442
X-RAY DIFFRACTIONf_plane_restr0.005516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.68590.5631240.47992378X-RAY DIFFRACTION95
1.6859-1.72510.40061180.39652585X-RAY DIFFRACTION99
1.7251-1.76830.39181220.3642541X-RAY DIFFRACTION99
1.7683-1.81610.35031270.32442567X-RAY DIFFRACTION99
1.8161-1.86950.39441300.29682495X-RAY DIFFRACTION100
1.8695-1.92990.2751410.25812588X-RAY DIFFRACTION100
1.9299-1.99880.25181540.21952532X-RAY DIFFRACTION100
1.9988-2.07890.25931540.20492536X-RAY DIFFRACTION100
2.0789-2.17350.25741310.18582546X-RAY DIFFRACTION100
2.1735-2.28810.22841300.17972564X-RAY DIFFRACTION100
2.2881-2.43140.22151570.17572547X-RAY DIFFRACTION100
2.4314-2.61910.19341360.1752558X-RAY DIFFRACTION100
2.6191-2.88260.22831250.18022564X-RAY DIFFRACTION100
2.8826-3.29950.20131260.17242597X-RAY DIFFRACTION100
3.2995-4.15630.18211480.16122550X-RAY DIFFRACTION100
4.1563-39.380.17941500.16762579X-RAY DIFFRACTION100
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)
11.248-2.3508-0.50294.78560.91450.7524-0.0774-0.0437-0.00730.14640.06580.05590.07230.02690.02680.3965-0.0094-0.00250.24180.00750.23935.276713.970521.1592
20.08150.49840.23475.86661.93441.1919-0.03420.02470.0066-0.19420.00080.0245-0.08050.02010.02880.3714-0.01390.01710.25450.01340.25013.656729.791615.6723
36.981-0.24781.41862.8294-1.52216.30030.00790.3176-0.137-0.25080.0330.13940.1924-0.3579-0.05010.52820.0150.04930.2612-0.02770.2613.30445.8899-1.6179
47.10650.4446-0.92163.2736-1.86674.2661-0.0037-0.2496-0.01940.19890.06220.1412-0.1603-0.2641-0.05280.52630.03610.0070.2439-0.02940.2313-7.828535.676836.5128
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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