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- PDB-5hk5: Structure of the Grem2-GDF5 Inhibitory Complex -

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Basic information

Entry
Database: PDB / ID: 5hk5
TitleStructure of the Grem2-GDF5 Inhibitory Complex
Components
  • Gremlin-2
  • Growth/differentiation factor 5
KeywordsCYTOKINE / DAN-family / Bone Morphogenetic Proteins
Function / homology
Function and homology information


sequestering of BMP from receptor via BMP binding / regulation of cytokine activity / determination of dorsal identity / ossification involved in bone remodeling / Signaling by BMP / embryonic body morphogenesis / forelimb morphogenesis / BMP binding / chondroblast differentiation / hindlimb morphogenesis ...sequestering of BMP from receptor via BMP binding / regulation of cytokine activity / determination of dorsal identity / ossification involved in bone remodeling / Signaling by BMP / embryonic body morphogenesis / forelimb morphogenesis / BMP binding / chondroblast differentiation / hindlimb morphogenesis / negative regulation of mesenchymal cell apoptotic process / 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 / positive regulation of SMAD protein signal transduction / negative regulation of BMP signaling pathway / regulation of multicellular organism growth / chondrocyte differentiation / BMP signaling pathway / response to mechanical stimulus / positive regulation of neuron differentiation / transforming growth factor beta receptor signaling pathway / cytokine activity / animal organ morphogenesis / growth factor activity / cytokine-mediated signaling pathway / negative regulation of epithelial cell proliferation / cell-cell signaling / heparin binding / negative regulation of neuron apoptotic process / receptor ligand activity / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Gremlin-1/2 / DAN / DAN domain / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. ...Gremlin-1/2 / DAN / DAN domain / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / 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 / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Gremlin-2 / Growth/differentiation factor 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsNolan, K. / Thompson, T.B. / Read, R.J.
Funding support United States, United Kingdom, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM114640 United States
American Heart Association14PRE20480142 United States
Wellcome Trust082961/Z/07/Z United Kingdom
CitationJournal: Cell Rep / Year: 2016
Title: Structure of Gremlin-2 in Complex with GDF5 Gives Insight into DAN-Family-Mediated BMP Antagonism.
Authors: Nolan, K. / Kattamuri, C. / Rankin, S.A. / Read, R.J. / Zorn, A.M. / Thompson, T.B.
History
DepositionJan 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Gremlin-2
F: Gremlin-2
G: Gremlin-2
H: Gremlin-2
A: Growth/differentiation factor 5
B: Growth/differentiation factor 5
C: Growth/differentiation factor 5
D: Growth/differentiation factor 5


Theoretical massNumber of molelcules
Total (without water)122,4248
Polymers122,4248
Non-polymers00
Water00
1
E: Gremlin-2
A: Growth/differentiation factor 5
C: Growth/differentiation factor 5

F: Gremlin-2


Theoretical massNumber of molelcules
Total (without water)61,2124
Polymers61,2124
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_585x+1/2,-y+3,-z+1/21
Buried area9650 Å2
ΔGint-73 kcal/mol
Surface area27200 Å2
MethodPISA
2
E: Gremlin-2
F: Gremlin-2
A: Growth/differentiation factor 5

C: Growth/differentiation factor 5


Theoretical massNumber of molelcules
Total (without water)61,2124
Polymers61,2124
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_485x-1/2,-y+3,-z+1/21
Buried area9150 Å2
ΔGint-49 kcal/mol
Surface area27700 Å2
MethodPISA
3
G: Gremlin-2
B: Growth/differentiation factor 5
D: Growth/differentiation factor 5

H: Gremlin-2


Theoretical massNumber of molelcules
Total (without water)61,2124
Polymers61,2124
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_475x-1/2,-y+2,-z+1/21
Buried area9000 Å2
ΔGint-69 kcal/mol
Surface area27210 Å2
MethodPISA
4
G: Gremlin-2
H: Gremlin-2
B: Growth/differentiation factor 5

D: Growth/differentiation factor 5


Theoretical massNumber of molelcules
Total (without water)61,2124
Polymers61,2124
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_575x+1/2,-y+2,-z+1/21
Buried area9080 Å2
ΔGint-46 kcal/mol
Surface area27130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.721, 125.791, 125.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein
Gremlin-2 / Cysteine knot superfamily 1 / BMP antagonist 2 / Protein related to DAN and cerberus / PRDC


Mass: 17007.482 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Grem2, Cktsf1b2, Prdc / Production host: Escherichia coli (E. coli) / References: UniProt: O88273
#2: 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: 13598.638 Da / Num. of mol.: 4
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

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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: 3.71 Å3/Da / Density % sol: 66.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: HEPES, ammonium chloride, ethylammonium nitrate / PH range: 7.5 - 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.032 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.032 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.517
11-H, L, K20.483
ReflectionResolution: 2.9→50.55 Å / Num. obs: 40910 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.068 / Net I/σ(I): 8 / Num. measured all: 271627 / Scaling rejects: 172
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.9-3.026.41.4671.61100
10.46-50.455.80.04416199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.12data scaling
PHASERphasing
REFMAC5.8.0124refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JPH, GDF5

4jph


Resolution: 2.9→50.55 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.901 / SU B: 10.6 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2824 2113 5.2 %RANDOM
Rwork0.2614 ---
obs0.2625 38807 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.47 Å2 / Biso mean: 36.641 Å2 / Biso min: 10.94 Å2
Baniso -1Baniso -2Baniso -3
1--4.17 Å20 Å20 Å2
2---14.7 Å20 Å2
3---18.87 Å2
Refinement stepCycle: final / Resolution: 2.9→50.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7425 0 0 0 7425
Num. residues----925
LS refinement shellResolution: 2.897→2.972 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 139 -
Rwork0.36 2729 -
all-2868 -
obs--95.22 %

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