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- PDB-6z3g: Repulsive Guidance Molecule A (RGMA) in complex with Growth Diffe... -

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Basic information

Entry
Database: PDB / ID: 6z3g
TitleRepulsive Guidance Molecule A (RGMA) in complex with Growth Differentiation Factor 5 (GDF5)
Components
  • Growth/differentiation factor 5
  • Repulsive guidance molecule A
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 collateral sprouting / negative regulation of axon regeneration / negative regulation of mesenchymal cell apoptotic process / Netrin-1 signaling / positive regulation of chondrocyte differentiation ...ossification involved in bone remodeling / forelimb morphogenesis / BMP binding / chondroblast differentiation / hindlimb morphogenesis / negative regulation of collateral sprouting / negative regulation of axon regeneration / negative regulation of mesenchymal cell apoptotic process / Netrin-1 signaling / positive regulation of chondrocyte differentiation / transferrin receptor binding / regulation of BMP signaling pathway / mesenchymal cell apoptotic process / positive regulation of BMP signaling pathway / positive regulation of membrane protein ectodomain proteolysis / negative regulation of chondrocyte differentiation / embryonic limb morphogenesis / Molecules associated with elastic fibres / membrane protein ectodomain proteolysis / positive regulation of SMAD protein signal transduction / regulation of multicellular organism growth / chondrocyte differentiation / BMP signaling pathway / response to mechanical stimulus / coreceptor activity / side of membrane / positive regulation of neuron differentiation / transforming growth factor beta receptor signaling pathway / cytokine activity / neural tube closure / growth factor activity / positive regulation of neuron projection development / negative regulation of epithelial cell proliferation / neuron projection development / cell-cell signaling / negative regulation of neuron apoptotic process / cell surface / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / 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
CITRIC ACID / Growth/differentiation factor 5 / Repulsive guidance molecule A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 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 1.4Nov 13, 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: Repulsive guidance molecule A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2263
Polymers25,0342
Non-polymers1921
Water00
1
A: Growth/differentiation factor 5
B: Repulsive guidance molecule A
hetero molecules

A: Growth/differentiation factor 5
B: Repulsive guidance molecule A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4536
Polymers50,0694
Non-polymers3842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/31
Buried area6520 Å2
ΔGint-61 kcal/mol
Surface area17440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.650, 97.650, 99.820
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 Repulsive guidance molecule A / RGM domain family member A


Mass: 11628.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RGMA, RGM / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q96B86
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
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: 2.74 Å3/Da / Density % sol: 55.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.5, 24% v/v polyethylene glycol (PEG) 400.

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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: 2.78→49.91 Å / Num. obs: 7375 / % possible obs: 97.8 % / Redundancy: 18.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 23.4
Reflection shellResolution: 2.78→2.85 Å / Rmerge(I) obs: 4.129 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 494 / CC1/2: 0.592

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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: 4UHY

4uhy


Resolution: 2.78→48.825 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2878 379 5.17 %
Rwork0.234 --
obs0.2365 7337 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.78→48.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1265 0 13 0 1278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051313
X-RAY DIFFRACTIONf_angle_d0.6241786
X-RAY DIFFRACTIONf_dihedral_angle_d7.531804
X-RAY DIFFRACTIONf_chiral_restr0.042194
X-RAY DIFFRACTIONf_plane_restr0.005230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7804-3.18260.36321260.31282173X-RAY DIFFRACTION95
3.1826-4.00950.32011280.26722295X-RAY DIFFRACTION99
4.0095-48.8250.2671250.21332490X-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)
12.2797-2.5503-0.52214.79234.29656.2090.05380.1060.1085-0.47830.1181-0.1329-0.41830.4438-0.20420.5945-0.17340.08720.7066-0.01360.472-44.002725.81219.7377
21.27740.06981.801200.13742.74430.48270.29170.25631.0831-0.3103-1.8007-0.75930.5073-0.00682.4832-0.4943-0.50692.0977-0.19942.269-29.167410.199221.014
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 397 through 501)
2X-RAY DIFFRACTION2(chain 'B' and resid 47 through 116)

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