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- PDB-3evs: Crystal structure of the GDF-5:BMP receptor IB complex. -

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Basic information

Entry
Database: PDB / ID: 3evs
TitleCrystal structure of the GDF-5:BMP receptor IB complex.
Components
  • Bone morphogenetic protein receptor type-1B
  • Growth/differentiation factor 5
KeywordsCYTOKINE/Transferase Receptor / ligand-receptor complex / cystin-knot ligand / three-finger toxn fold (receptor) / Cleavage on pair of basic residues / Cytokine / Disease mutation / Dwarfism / Glycoprotein / Growth factor / Secreted / ATP-binding / Kinase / Magnesium / Manganese / Membrane / Metal-binding / Nucleotide-binding / Receptor / Serine/threonine-protein kinase / Transferase / Transmembrane / CYTOKINE-Transferase Receptor COMPLEX
Function / homology
Function and homology information


ossification involved in bone remodeling / ovarian cumulus expansion / negative regulation of chondrocyte proliferation / Signaling by BMP / forelimb morphogenesis / chondrocyte development / estrogen biosynthetic process / central nervous system neuron differentiation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / BMP binding ...ossification involved in bone remodeling / ovarian cumulus expansion / negative regulation of chondrocyte proliferation / Signaling by BMP / forelimb morphogenesis / chondrocyte development / estrogen biosynthetic process / central nervous system neuron differentiation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / BMP binding / chondroblast differentiation / proteoglycan biosynthetic process / hindlimb morphogenesis / positive regulation of cartilage development / negative regulation of mesenchymal cell apoptotic process / endochondral bone morphogenesis / transforming growth factor beta receptor activity / positive regulation of chondrocyte differentiation / BMP receptor activity / mesenchymal cell apoptotic process / transforming growth factor beta receptor activity, type I / eye development / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / positive regulation of BMP signaling pathway / camera-type eye development / dorsal/ventral pattern formation / negative regulation of chondrocyte differentiation / embryonic limb morphogenesis / ovulation cycle / Molecules associated with elastic fibres / cell surface receptor protein serine/threonine kinase signaling pathway / cartilage condensation / retinal ganglion cell axon guidance / SMAD binding / positive regulation of SMAD protein signal transduction / regulation of multicellular organism growth / BMP signaling pathway / chondrocyte differentiation / positive regulation of osteoblast differentiation / positive regulation of bone mineralization / response to mechanical stimulus / positive regulation of neuron differentiation / transforming growth factor beta receptor signaling pathway / cytokine activity / growth factor activity / bone development / cellular response to growth factor stimulus / osteoblast differentiation / negative regulation of epithelial cell proliferation / cell-cell signaling / retina development in camera-type eye / negative regulation of neuron apoptotic process / cell differentiation / receptor complex / inflammatory response / neuronal cell body / dendrite / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / ATP binding / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Transforming growth factor-beta-related / Activin types I and II receptor domain ...TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Transforming growth factor-beta-related / Activin types I and II receptor domain / Activin types I and II receptor domain / 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 / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / Snake toxin-like superfamily / Ribbon / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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 / Mainly Beta
Similarity search - Domain/homology
Bone morphogenetic protein receptor type-1B / Growth/differentiation factor 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsKotzsch, A. / Mueller, T.D.
CitationJournal: Embo J. / Year: 2009
Title: Crystal structure analysis reveals a spring-loaded latch as molecular mechanism for GDF-5-type I receptor specificity.
Authors: Kotzsch, A. / Nickel, J. / Seher, A. / Sebald, W. / Muller, T.D.
History
DepositionOct 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 16, 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
B: Growth/differentiation factor 5
C: Bone morphogenetic protein receptor type-1B


Theoretical massNumber of molelcules
Total (without water)26,6202
Polymers26,6202
Non-polymers00
Water91951
1
B: Growth/differentiation factor 5
C: Bone morphogenetic protein receptor type-1B

B: Growth/differentiation factor 5
C: Bone morphogenetic protein receptor type-1B


Theoretical massNumber of molelcules
Total (without water)53,2414
Polymers53,2414
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area6970 Å2
ΔGint-53 kcal/mol
Surface area18260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.455, 76.455, 82.784
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Growth/differentiation factor 5 / GDF-5 / Cartilage-derived morphogenetic protein 1 / CDMP-1 / Radotermin


Mass: 13405.481 Da / Num. of mol.: 1 / Fragment: UNP residues 387-501
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: U2OS / Gene: CDMP1, GDF5 / Plasmid: RBSIIN25x/o / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P43026
#2: Protein Bone morphogenetic protein receptor type-1B / Serine/threonine-protein kinase receptor R6 / SKR6 / Activin receptor-like kinase 6 / ALK-6


Mass: 13214.857 Da / Num. of mol.: 1 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Acvrlk6, Bmpr1b / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): AD494(DE3) / References: UniProt: P36898
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.2745.87
2
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 5.25
Details: 0.1M sodium acetate, 50% PPG 400, 30mM magnesium sulfate, pH 5.25, VAPOR DIFFUSION, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA11.10485
SYNCHROTRONBESSY 14.120.97962, 0.97979, 0.90789
Detector
TypeIDDetectorDateDetails
MARMOSAIC 225 mm CCD1CCDJun 5, 2006mirrors
MARMOSAIC 225 mm CCD2CCDMar 7, 2007mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si-111 crystalSINGLE WAVELENGTHMx-ray1
2Si-111 crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.104851
20.979621
30.979791
40.907891
ReflectionRedundancy: 6.75 % / Number: 54117 / Rmerge(I) obs: 0.1 / Χ2: 0.97 / D res high: 2.6 Å / D res low: 38.31 Å / Num. obs: 7954 / % possible obs: 99.9
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
5.638.3199.30.0670.826.1331
4.445.699.80.0680.716.6518
3.884.441000.0750.696.7910
3.533.8899.90.0990.86.819
3.283.531000.1270.826.8526
3.083.281000.1620.996.8831
2.933.081000.2211.086.8942
2.82.931000.2831.196.942
2.692.81000.341.296.8787
2.62.691000.4081.36.85100
ReflectionResolution: 2.1→34.19 Å / Num. all: 15897 / Num. obs: 14815 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.66 % / Rmerge(I) obs: 0.071 / Χ2: 0.99 / Scaling rejects: 1082
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 9.87 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 5.3 / Num. measured all: 14428 / Num. unique all: 1455 / Χ2: 1.19 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_12.0338.310064051540
ISO_22.0338.310.2390.1846031234
ISO_32.0338.310.4670.33245851227
ISO_42.0338.310.4980.37163751482
ANO_12.0338.310.727064040
ANO_22.0338.310.254046050
ANO_32.0338.310.286045890
ANO_42.0338.310.1460134070
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_18.86-38.3100119122
ISO_16.35-8.8600250122
ISO_15.21-6.3500342124
ISO_14.52-5.2100402121
ISO_14.05-4.5200474132
ISO_13.7-4.0500525129
ISO_13.43-3.700580125
ISO_13.21-3.4300625125
ISO_13.03-3.2100666133
ISO_12.87-3.0300712128
ISO_12.74-2.8700745119
ISO_12.62-2.7400795136
ISO_12.52-2.620017024
ISO_12.43-2.520000
ISO_12.35-2.430000
ISO_12.27-2.350000
ISO_12.21-2.270000
ISO_12.14-2.210000
ISO_12.09-2.140000
ISO_12.03-2.090000
ANO_18.86-38.311.95301180
ANO_16.35-8.861.87902500
ANO_15.21-6.351.62403420
ANO_14.52-5.211.40204020
ANO_14.05-4.521.08904740
ANO_13.7-4.050.66605250
ANO_13.43-3.70.63905800
ANO_13.21-3.430.48906250
ANO_13.03-3.210.43506660
ANO_12.87-3.030.36107120
ANO_12.74-2.870.26407450
ANO_12.62-2.740.23407950
ANO_12.52-2.620.22601700
ANO_12.43-2.520000
ANO_12.35-2.430000
ANO_12.27-2.350000
ANO_12.21-2.270000
ANO_12.14-2.210000
ANO_12.09-2.140000
ANO_12.03-2.090000
ISO_28.86-38.310.8870.265119120
ISO_26.35-8.860.6890.439250121
ISO_25.21-6.350.5630.303341124
ISO_24.52-5.210.4390.185401121
ISO_24.05-4.520.3120.176474131
ISO_23.7-4.050.2320.141525129
ISO_23.43-3.70.1840.111580125
ISO_23.21-3.430.1360.07625122
ISO_23.03-3.210.1070.075666130
ISO_22.87-3.030.0730.052622111
ISO_22.74-2.870000
ISO_22.62-2.740000
ISO_22.52-2.620000
ISO_22.43-2.520000
ISO_22.35-2.430000
ISO_22.27-2.350000
ISO_22.21-2.270000
ISO_22.14-2.210000
ISO_22.09-2.140000
ISO_22.03-2.090000
ANO_28.86-38.310.87801190
ANO_26.35-8.860.63702490
ANO_25.21-6.350.52703410
ANO_24.52-5.210.40804000
ANO_24.05-4.520.3104740
ANO_23.7-4.050.21105250
ANO_23.43-3.70.17605800
ANO_23.21-3.430.13106250
ANO_23.03-3.210.1206670
ANO_22.87-3.030.09906250
ANO_22.74-2.870000
ANO_22.62-2.740000
ANO_22.52-2.620000
ANO_22.43-2.520000
ANO_22.35-2.430000
ANO_22.27-2.350000
ANO_22.21-2.270000
ANO_22.14-2.210000
ANO_22.09-2.140000
ANO_22.03-2.090000
ISO_38.86-38.311.2610.464119120
ISO_36.35-8.860.910.61250121
ISO_35.21-6.350.9820.542342123
ISO_34.52-5.210.8090.572402121
ISO_34.05-4.520.5940.213474129
ISO_33.7-4.050.4170.317525128
ISO_33.43-3.70.330.225580124
ISO_33.21-3.430.2760.153624124
ISO_33.03-3.210.210.119666131
ISO_32.87-3.030.1580.096603106
ISO_32.74-2.870000
ISO_32.62-2.740000
ISO_32.52-2.620000
ISO_32.43-2.520000
ISO_32.35-2.430000
ISO_32.27-2.350000
ISO_32.21-2.270000
ISO_32.14-2.210000
ISO_32.09-2.140000
ISO_32.03-2.090000
ANO_38.86-38.311.12501190
ANO_36.35-8.860.44402500
ANO_35.21-6.350.60703420
ANO_34.52-5.210.50404020
ANO_34.05-4.520.34904740
ANO_33.7-4.050.24405250
ANO_33.43-3.70.18905800
ANO_33.21-3.430.15106240
ANO_33.03-3.210.13906670
ANO_32.87-3.030.11406060
ANO_32.74-2.870000
ANO_32.62-2.740000
ANO_32.52-2.620000
ANO_32.43-2.520000
ANO_32.35-2.430000
ANO_32.27-2.350000
ANO_32.21-2.270000
ANO_32.14-2.210000
ANO_32.09-2.140000
ANO_32.03-2.090000
ISO_48.86-38.310.4860.4739087
ISO_46.35-8.860.5180.382249113
ISO_45.21-6.350.510.313342117
ISO_44.52-5.210.4180.295402116
ISO_44.05-4.520.3260.19474132
ISO_43.7-4.050.2770.231525128
ISO_43.43-3.70.2670.209580125
ISO_43.21-3.430.240.185625125
ISO_43.03-3.210.2260.164666133
ISO_42.87-3.030.2110.147712127
ISO_42.74-2.870.1970.15745119
ISO_42.62-2.740.1710.153795136
ISO_42.52-2.620.2090.11617024
ISO_42.43-2.520000
ISO_42.35-2.430000
ISO_42.27-2.350000
ISO_42.21-2.270000
ISO_42.14-2.210000
ISO_42.09-2.140000
ISO_42.03-2.090000
ANO_48.86-38.310.4790820
ANO_46.35-8.860.41502450
ANO_45.21-6.350.44103420
ANO_44.52-5.210.3204020
ANO_44.05-4.520.21204740
ANO_43.7-4.050.16805250
ANO_43.43-3.70.14205800
ANO_43.21-3.430.13206250
ANO_43.03-3.210.10806670
ANO_42.87-3.030.09407150
ANO_42.74-2.870.06907460
ANO_42.62-2.740.05607950
ANO_42.52-2.620.04108120
ANO_42.43-2.520.03208680
ANO_42.35-2.430.02808810
ANO_42.27-2.350.02109380
ANO_42.21-2.270.01609430
ANO_42.14-2.210.014010000
ANO_42.09-2.140.011010030
ANO_42.03-2.090.00807640
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 15945
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.81-10058.80.803502
5.34-6.8162.90.877506
4.63-5.34630.897503
4.18-4.6363.90.918502
3.87-4.1865.60.908501
3.63-3.8768.10.897518
3.44-3.6372.40.881509
3.28-3.4478.40.879511
3.14-3.2875.10.864543
3.02-3.1481.70.826541
2.92-3.02810.85570
2.82-2.9281.40.841582
2.73-2.82840.835605
2.65-2.7385.40.823627
2.58-2.6586.50.831635
2.51-2.5889.30.823658
2.45-2.5190.80.834671
2.39-2.4588.20.837687
2.34-2.39920.824717
2.28-2.3489.10.8706
2.24-2.2888.90.815734
2.19-2.2492.40.815739
2.15-2.1992.40.731767
2.11-2.1593.90.693769
2.07-2.1188.80.721781
2.03-2.07880.695561

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
SHARPphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→34.19 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.335 / WRfactor Rwork: 0.283 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.832 / SU B: 10.02 / SU ML: 0.128 / SU R Cruickshank DPI: 0.264 / SU Rfree: 0.234 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.181 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 752 5.1 %RANDOM
Rwork0.215 ---
all0.217 15897 --
obs0.217 14814 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 114.78 Å2 / Biso mean: 71.871 Å2 / Biso min: 40.39 Å2
Baniso -1Baniso -2Baniso -3
1--2.81 Å20 Å20 Å2
2---2.81 Å20 Å2
3---5.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.181 Å0.203 Å
Refinement stepCycle: LAST / Resolution: 2.1→34.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1483 0 0 51 1534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211528
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.9612083
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7285187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45324.30672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.70515251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0311510
X-RAY DIFFRACTIONr_chiral_restr0.1110.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021178
X-RAY DIFFRACTIONr_nbd_refined0.2570.3607
X-RAY DIFFRACTIONr_nbtor_refined0.3250.51043
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.5117
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3570.355
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2960.522
X-RAY DIFFRACTIONr_mcbond_it1.2491.5965
X-RAY DIFFRACTIONr_mcangle_it2.12621557
X-RAY DIFFRACTIONr_scbond_it2.9693610
X-RAY DIFFRACTIONr_scangle_it3.9964.5526
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 51 -
Rwork0.289 1016 -
all-1067 -
obs-1016 100 %
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)
18.64643.18841.53013.58280.82910.9053-0.12480.5971-0.3053-0.11610.251-0.2677-0.0960.113-0.1263-0.1995-0.03780.0311-0.2046-0.0081-0.41758.907537.361126.3631
28.40131.2836-1.21111.7964-1.83336.33460.14210.33350.9998-0.01440.0936-0.0009-0.5937-0.2037-0.2357-0.1496-0.06950.0596-0.22110.0626-0.102310.279861.107724.7935
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B17 - 120
2X-RAY DIFFRACTION2C16 - 21
3X-RAY DIFFRACTION2C31 - 45
4X-RAY DIFFRACTION2C50 - 72
5X-RAY DIFFRACTION2C77 - 100

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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