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- PDB-6z3l: Repulsive Guidance Molecule C (RGMC, Hemojuvelin, HJV, HFE2) in c... -

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Basic information

Entry
Database: PDB / ID: 6z3l
TitleRepulsive Guidance Molecule C (RGMC, Hemojuvelin, HJV, HFE2) in complex with Growth Differentiation Factor 5 (GDF5)
Components
  • Growth/differentiation factor 5
  • Hemojuvelin
KeywordsSIGNALING PROTEIN / Repulsive Guidance Molecule / RGM / Bone Morphogenetic Protein / BMP / Growth Differentiation Factor 5 / GDF5 / Neogenin / axon guidance / TGFbeta signalling / brain development / iron metabolism / Hemojuvelin / HJV / HFE2 / hemochromatosis type 2 protein / juvenile hemochromatosis.
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 / BMP receptor complex / transferrin receptor binding ...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 / BMP receptor complex / transferrin receptor binding / mesenchymal cell apoptotic process / cellular response to BMP stimulus / plasma membrane protein complex / activin receptor signaling pathway / positive regulation of BMP signaling pathway / negative regulation of chondrocyte differentiation / embryonic limb morphogenesis / Molecules associated with elastic fibres / protein autoprocessing / negative regulation of BMP signaling pathway / 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 / growth factor activity / HFE-transferrin receptor complex / multicellular organismal-level iron ion homeostasis / negative regulation of epithelial cell proliferation / cell-cell signaling / negative regulation of neuron apoptotic process / transcription by RNA polymerase II / intracellular iron ion homeostasis / signaling receptor binding / negative regulation of transcription by RNA polymerase II / cell surface / 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-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 / Hemojuvelin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.513 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

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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: Hemojuvelin


Theoretical massNumber of molelcules
Total (without water)25,8072
Polymers25,8072
Non-polymers00
Water21612
1
A: Growth/differentiation factor 5
B: Hemojuvelin

A: Growth/differentiation factor 5
B: Hemojuvelin


Theoretical massNumber of molelcules
Total (without water)51,6154
Polymers51,6154
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area5980 Å2
ΔGint-55 kcal/mol
Surface area16580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.820, 98.820, 99.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-609-

HOH

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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 Hemojuvelin / Hemochromatosis type 2 protein / Hemojuvelin BMP coreceptor / RGM domain family member C


Mass: 12401.993 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HJV, HFE2, RGMC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q6ZVN8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
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: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 1 M LiCl, 0.1 M citric acid pH 4.0, 8% gamma-butyrolactone.
PH range: 4.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.5→85.58 Å / Num. obs: 10324 / % possible obs: 99 % / Redundancy: 47.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 23.9
Reflection shellResolution: 2.5→2.56 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 721 / Rpim(I) all: 1.125

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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: 4UI1

4ui1


Resolution: 2.513→85.58 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2673 471 5.3 %
Rwork0.2378 --
obs0.2395 8883 86.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.513→85.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 0 12 1232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021264
X-RAY DIFFRACTIONf_angle_d0.3861721
X-RAY DIFFRACTIONf_dihedral_angle_d13.778779
X-RAY DIFFRACTIONf_chiral_restr0.037191
X-RAY DIFFRACTIONf_plane_restr0.002223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5134-2.87720.36461030.36441879X-RAY DIFFRACTION60
2.8772-3.6250.30041700.26613170X-RAY DIFFRACTION99
3.625-85.580.24171980.21123363X-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)
16.58092.51272.3732.79151.31263.12760.0867-0.2853-0.3893-0.01060.0420.02930.4526-0.1808-0.1370.44270.05120.0090.24910.02540.2163-44.719825.85086.9237
24.8420.5672-1.0141.41590.63380.7255-0.5747-1.1818-0.78150.69910.782-1.38550.86790.6189-0.18691.99180.3208-0.01032.2658-0.17951.4792-24.793224.0529-6.0867
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 36 through 120)

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