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- PDB-7mrz: Structure of GDF11 bound to fused ActRIIB-ECD and Alk4-ECD with A... -

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Basic information

Entry
Database: PDB / ID: 7mrz
TitleStructure of GDF11 bound to fused ActRIIB-ECD and Alk4-ECD with Anti-ActRIIB Fab fragment
Components
  • Activin receptor type-2B,Activin receptor type-1B
  • Fab Heavy Chain
  • Fab Light Chain
  • Growth/differentiation factor 11
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / Growth factor / type I receptor / Transforming growth factor beta / type II receptor / ternary complex / GDF11 / SIGNALING PROTEIN / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


spinal cord anterior/posterior patterning / type B pancreatic cell maturation / negative regulation of amacrine cell differentiation / Regulation of signaling by NODAL / inhibin binding / activin receptor activity, type II / amacrine cell differentiation / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway / nodal signaling pathway ...spinal cord anterior/posterior patterning / type B pancreatic cell maturation / negative regulation of amacrine cell differentiation / Regulation of signaling by NODAL / inhibin binding / activin receptor activity, type II / amacrine cell differentiation / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway / nodal signaling pathway / activin receptor activity / venous blood vessel development / lymphangiogenesis / retina vasculature development in camera-type eye / positive regulation of trophoblast cell migration / activin receptor activity, type I / embryonic foregut morphogenesis / activin receptor complex / camera-type eye morphogenesis / artery development / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / Signaling by BMP / activin binding / activin receptor signaling pathway / SMAD protein signal transduction / Signaling by Activin / metanephros development / kinase activator activity / Signaling by NODAL / gastrulation with mouth forming second / pancreas development / determination of left/right symmetry / skeletal system morphogenesis / negative regulation of cold-induced thermogenesis / insulin secretion / anterior/posterior pattern specification / ureteric bud development / cell surface receptor protein serine/threonine kinase signaling pathway / organ growth / roof of mouth development / SMAD binding / growth factor binding / odontogenesis of dentin-containing tooth / mesoderm development / positive regulation of SMAD protein signal transduction / hair follicle development / blood vessel remodeling / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / response to glucose / extrinsic apoptotic signaling pathway / protein serine/threonine/tyrosine kinase activity / post-embryonic development / positive regulation of erythrocyte differentiation / kidney development / skeletal system development / cytokine activity / peptidyl-threonine phosphorylation / growth factor activity / lung development / negative regulation of cell growth / cellular response to growth factor stimulus / G1/S transition of mitotic cell cycle / nervous system development / heart development / in utero embryonic development / cell population proliferation / protein autophosphorylation / receptor complex / phosphorylation / negative regulation of cell population proliferation / protein phosphorylation / negative regulation of gene expression / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / ubiquitin protein ligase binding / positive regulation of gene expression / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / cell surface / signal transduction / protein-containing complex / extracellular space / nucleoplasm / ATP binding / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Transforming growth factor-beta (TGF-beta) family ...TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Transforming growth factor-beta (TGF-beta) family / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Cystine-knot cytokine / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Growth/differentiation factor 11 / Activin receptor type-1B / Activin receptor type-2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsGoebel, E.J. / Kattamuri, C. / Gipson, G.R. / Thompson, T.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM134923-02 United States
CitationJournal: Iscience / Year: 2022
Title: Structures of activin ligand traps using natural sets of type I and type II TGF beta receptors.
Authors: Goebel, E.J. / Kattamuri, C. / Gipson, G.R. / Krishnan, L. / Chavez, M. / Czepnik, M. / Maguire, M.C. / Grenha, R. / Hakansson, M. / Logan, D.T. / Grinberg, A.V. / Sako, D. / Castonguay, R. ...Authors: Goebel, E.J. / Kattamuri, C. / Gipson, G.R. / Krishnan, L. / Chavez, M. / Czepnik, M. / Maguire, M.C. / Grenha, R. / Hakansson, M. / Logan, D.T. / Grinberg, A.V. / Sako, D. / Castonguay, R. / Kumar, R. / Thompson, T.B.
History
DepositionMay 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Growth/differentiation factor 11
C: Activin receptor type-2B,Activin receptor type-1B
X: Fab Heavy Chain
Y: Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3726
Polymers88,0554
Non-polymers3172
Water00
1
A: Growth/differentiation factor 11
C: Activin receptor type-2B,Activin receptor type-1B
X: Fab Heavy Chain
Y: Fab Light Chain
hetero molecules

A: Growth/differentiation factor 11
C: Activin receptor type-2B,Activin receptor type-1B
X: Fab Heavy Chain
Y: Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,74412
Polymers176,1098
Non-polymers6354
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area20320 Å2
ΔGint-153 kcal/mol
Surface area68010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.261, 68.261, 990.380
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)

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Components

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Protein , 2 types, 2 molecules AC

#1: Protein Growth/differentiation factor 11 / GDF-11 / Bone morphogenetic protein 11 / BMP-11


Mass: 12471.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GDF11, BMP11 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: O95390
#2: Protein Activin receptor type-2B,Activin receptor type-1B / ACTR-IIB fused to Activin receptor-like kinase 4


Mass: 27952.279 Da / Num. of mol.: 1
Fragment: Extracellular domains of both proteins in the fused construct
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR2B, ACVR1B, ACVRLK4, ALK4 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: Q13705, UniProt: P36896, receptor protein serine/threonine kinase

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Antibody , 2 types, 2 molecules XY

#3: Antibody Fab Heavy Chain


Mass: 23427.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody Fab Light Chain


Mass: 24203.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Sugars / Non-polymers , 2 types, 2 molecules

#5: 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
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
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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Details

Has ligand of interestN

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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: 3.95 Å3/Da / Density % sol: 68.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M HEPES, 0.9M ammonium sulfate, 0.9 M KCl

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033202 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033202 Å / Relative weight: 1
ReflectionResolution: 3→49.51 Å / Num. obs: 29791 / % possible obs: 99 % / Redundancy: 8 % / Biso Wilson estimate: 88.97 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.052 / Rrim(I) all: 0.189 / Net I/σ(I): 8.1 / Num. measured all: 237557 / Scaling rejects: 252
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3-3.184.30.3151919044930.7740.160.3562.896.8
9-49.5115.30.1462176014220.9920.0350.1514.199.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MAC

6mac


Resolution: 3→48.06 Å / SU ML: 0.5519 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.4425
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3271 1409 4.79 %
Rwork0.2884 28005 -
obs0.2902 29414 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.16 Å2
Refinement stepCycle: LAST / Resolution: 3→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5568 0 19 0 5587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00265717
X-RAY DIFFRACTIONf_angle_d0.63137770
X-RAY DIFFRACTIONf_chiral_restr0.043854
X-RAY DIFFRACTIONf_plane_restr0.0041003
X-RAY DIFFRACTIONf_dihedral_angle_d17.54482071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.110.35131200.35692702X-RAY DIFFRACTION96.31
3.11-3.230.38071290.32232575X-RAY DIFFRACTION96.26
3.23-3.380.3661570.32062629X-RAY DIFFRACTION96.8
3.38-3.560.35621360.33612724X-RAY DIFFRACTION98.89
3.56-3.780.40831400.33062766X-RAY DIFFRACTION99.35
3.78-4.070.36911570.31272742X-RAY DIFFRACTION99.49
4.07-4.480.32551390.28022804X-RAY DIFFRACTION99.93
4.48-5.130.24561200.27252908X-RAY DIFFRACTION99.97
5.13-6.460.33471550.2792914X-RAY DIFFRACTION99.97
6.46-48.060.29451560.25593241X-RAY DIFFRACTION99.94
Refinement TLS params.Method: refined / Origin x: -3.13491701418 Å / Origin y: -13.2630231103 Å / Origin z: -39.73890755 Å
111213212223313233
T0.790802647065 Å2-0.191020420261 Å20.0570288383319 Å2-0.504711509962 Å2-0.248891221839 Å2--0.93440869822 Å2
L0.344762311414 °2-0.276971725085 °20.568316915703 °2-0.374704849712 °2-0.867967282803 °2--2.10806205522 °2
S-0.0338595000185 Å °0.0766946088023 Å °-0.0532203920966 Å °-0.28553681605 Å °0.110855293134 Å °-0.0675233998469 Å °0.199754510354 Å °-0.0726201930396 Å °-0.0977468152237 Å °
Refinement TLS groupSelection details: all

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