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- PDB-5zok: Crystal structure of human SMAD1-MAN1 complex. -

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Basic information

Entry
Database: PDB / ID: 5zok
TitleCrystal structure of human SMAD1-MAN1 complex.
Components
  • Inner nuclear membrane protein Man1Nuclear envelope
  • Mothers against decapentaplegic homolog 1
KeywordsDNA BINDING PROTEIN / Transcription / Complex / TGF-beta signaling
Function / homology
Function and homology information


mesodermal cell fate commitment / homomeric SMAD protein complex / osteoblast fate commitment / SMAD protein complex / RUNX2 regulates bone development / co-SMAD binding / heteromeric SMAD protein complex / negative regulation of muscle cell differentiation / Depolymerization of the Nuclear Lamina / positive regulation of cartilage development ...mesodermal cell fate commitment / homomeric SMAD protein complex / osteoblast fate commitment / SMAD protein complex / RUNX2 regulates bone development / co-SMAD binding / heteromeric SMAD protein complex / negative regulation of muscle cell differentiation / Depolymerization of the Nuclear Lamina / positive regulation of cartilage development / primary miRNA binding / DEAD/H-box RNA helicase binding / Nuclear Envelope Breakdown / gamete generation / hindbrain development / cardiac conduction system development / primary miRNA processing / Signaling by BMP / embryonic pattern specification / negative regulation of activin receptor signaling pathway / SMAD protein signal transduction / Initiation of Nuclear Envelope (NE) Reformation / U1 snRNP binding / RHOD GTPase cycle / I-SMAD binding / cartilage development / Cardiogenesis / RND1 GTPase cycle / nuclear inner membrane / RND2 GTPase cycle / RND3 GTPase cycle / cardiac muscle cell proliferation / ureteric bud development / midbrain development / homeostatic process / positive regulation of sprouting angiogenesis / cellular response to organic cyclic compound / negative regulation of BMP signaling pathway / RHOG GTPase cycle / anatomical structure morphogenesis / RAC2 GTPase cycle / RAC3 GTPase cycle / BMP signaling pathway / positive regulation of osteoblast differentiation / RAC1 GTPase cycle / ossification / transforming growth factor beta receptor signaling pathway / negative regulation of transforming growth factor beta receptor signaling pathway / bone development / positive regulation of miRNA transcription / MAPK cascade / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / transcription by RNA polymerase II / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / DNA-templated transcription / ubiquitin protein ligase binding / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / protein kinase binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / membrane / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
MAN1, RNA recognition motif / MAN1, winged-helix domain / Man1/Src1, C-terminal / Man1-Src1p-C-terminal domain / Tumour Suppressor Smad4 - #10 / LEM domain / LEM domain / LEM domain profile. / in nuclear membrane-associated proteins / LEM/LEM-like domain superfamily ...MAN1, RNA recognition motif / MAN1, winged-helix domain / Man1/Src1, C-terminal / Man1-Src1p-C-terminal domain / Tumour Suppressor Smad4 - #10 / LEM domain / LEM domain / LEM domain profile. / in nuclear membrane-associated proteins / LEM/LEM-like domain superfamily / MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / MAD homology domain 1 (MH1) profile. / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. / Domain B in dwarfin family proteins / MAD homology 1, Dwarfin-type / MH1 domain / Domain A in dwarfin family proteins / SMAD-like domain superfamily / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Mothers against decapentaplegic homolog 1 / Inner nuclear membrane protein Man1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.85 Å
AuthorsMiyazono, K. / Ito, T. / Tanokura, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15K14708 Japan
Japan Society for the Promotion of Science17K19581 Japan
Japan Society for the Promotion of Science23228003 Japan
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural basis for receptor-regulated SMAD recognition by MAN1
Authors: Miyazono, K.I. / Ohno, Y. / Wada, H. / Ito, T. / Fukatsu, Y. / Kurisaki, A. / Asashima, M. / Tanokura, M.
History
DepositionApr 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mothers against decapentaplegic homolog 1
B: Inner nuclear membrane protein Man1
C: Mothers against decapentaplegic homolog 1
D: Inner nuclear membrane protein Man1


Theoretical massNumber of molelcules
Total (without water)77,2414
Polymers77,2414
Non-polymers00
Water0
1
A: Mothers against decapentaplegic homolog 1
B: Inner nuclear membrane protein Man1

A: Mothers against decapentaplegic homolog 1
B: Inner nuclear membrane protein Man1

A: Mothers against decapentaplegic homolog 1
B: Inner nuclear membrane protein Man1


Theoretical massNumber of molelcules
Total (without water)115,8626
Polymers115,8626
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
2
C: Mothers against decapentaplegic homolog 1
D: Inner nuclear membrane protein Man1

C: Mothers against decapentaplegic homolog 1
D: Inner nuclear membrane protein Man1

C: Mothers against decapentaplegic homolog 1
D: Inner nuclear membrane protein Man1


Theoretical massNumber of molelcules
Total (without water)115,8626
Polymers115,8626
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Unit cell
Length a, b, c (Å)187.050, 187.050, 187.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12(chain B and (resid 762 through 774 or resid 778 through 888))
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUGLUGLUchain AAA266 - 46510 - 209
211GLUGLUGLUGLUchain CCC266 - 46510 - 209
112SERSERARGARG(chain B and (resid 762 through 774 or resid 778 through 888))BB762 - 7744 - 16
122PROPROSERSER(chain B and (resid 762 through 774 or resid 778 through 888))BB778 - 88820 - 130
212SERSERSERSERchain DDD762 - 8884 - 130

NCS ensembles :
ID
1
2

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Components

#1: Protein Mothers against decapentaplegic homolog 1 / / Mothers against DPP homolog 1 / JV4-1 / Mad-related protein 1 / SMAD family member 1 / hSMAD1 / ...Mothers against DPP homolog 1 / JV4-1 / Mad-related protein 1 / SMAD family member 1 / hSMAD1 / Transforming growth factor-beta-signaling protein 1 / BSP-1


Mass: 23650.561 Da / Num. of mol.: 2 / Fragment: UNP residues 259-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15797
#2: Protein Inner nuclear membrane protein Man1 / Nuclear envelope / LEM domain-containing protein 3


Mass: 14970.151 Da / Num. of mol.: 2 / Fragment: UNP residues 762-890
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2U8

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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: 3.53 Å3/Da / Density % sol: 65.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 0.1M MES, 10% PEG20,000

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jul 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.85→46.76 Å / Num. obs: 26645 / % possible obs: 99.6 % / Redundancy: 6 % / Biso Wilson estimate: 61.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.042 / Rrim(I) all: 0.106 / Net I/σ(I): 15.5 / Num. measured all: 160567
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.85-35.90.79137750.7350.350.86798.9
9.01-46.765.40.0229300.9990.010.02495.9

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.12rc2_2821: ???refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementResolution: 2.85→42.912 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0.09 / Phase error: 26.36
RfactorNum. reflection% reflection
Rfree0.2549 2486 5.06 %
Rwork0.2149 --
obs0.2169 26574 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 170.49 Å2 / Biso mean: 70.4851 Å2 / Biso min: 29.02 Å2
Refinement stepCycle: final / Resolution: 2.85→42.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5213 0 0 0 5213
Num. residues----651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035356
X-RAY DIFFRACTIONf_angle_d0.6187265
X-RAY DIFFRACTIONf_chiral_restr0.045775
X-RAY DIFFRACTIONf_plane_restr0.005939
X-RAY DIFFRACTIONf_dihedral_angle_d12.0623158
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1861X-RAY DIFFRACTION12.278TORSIONAL
12C1861X-RAY DIFFRACTION12.278TORSIONAL
21B1098X-RAY DIFFRACTION12.278TORSIONAL
22D1098X-RAY DIFFRACTION12.278TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8485-2.90330.30721200.30912506262696
2.9033-2.96250.34721340.295226192753100
2.9625-3.02690.32571290.294226252754100
3.0269-3.09730.36311330.280726172750100
3.0973-3.17480.28991470.305925842731100
3.1748-3.26060.33511270.280426062733100
3.2606-3.35650.27951260.250626372763100
3.3565-3.46480.30691500.243825982748100
3.4648-3.58860.32021290.232226122741100
3.5886-3.73220.25271530.234625932746100
3.7322-3.90190.26531500.220325782728100
3.9019-4.10750.25851550.204725942749100
4.1075-4.36460.19651210.179426242745100
4.3646-4.70120.20271360.174926142750100
4.7012-5.17360.21511330.161825982731100
5.1736-5.92050.23311450.193825952740100
5.9205-7.45290.22551480.21252582273099
7.4529-42.91710.23161500.18162457260794
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)
17.53530.97733.43938.17622.04348.73150.07050.22520.303-0.1088-0.3013-0.09010.560.22270.31930.3023-0.02240.00710.2630.06340.40435.58919.13725.8638
26.73074.00893.3246.62944.84273.63180.0126-0.4243-0.778-0.01860.07590.42370.5665-0.2841-0.11670.4689-0.0775-0.00770.38140.03410.4153-1.90416.55095.9117
37.3341-2.72615.57447.3552-6.14997.92240.2309-0.2263-0.2153-0.15520.22550.36540.322-0.1304-0.52310.33160.0080.0570.44930.00320.301-0.886216.111316.2064
45.3597-4.44766.39636.7648-3.71328.5617-0.5472-2.19550.03091.01290.9030.6515-0.2708-0.7405-0.25160.70660.06880.05980.6116-0.05840.49730.008726.900324.2008
53.9067-1.0937-3.15281.91791.32935.10260.24380.15390.4681-0.3301-0.0531-0.0028-0.4521-0.1285-0.20480.472-0.0051-0.06830.28220.02320.38823.234931.4308-1.2676
64.2255-1.6374-2.57642.83821.99958.69510.1055-0.03910.47810.07110.1097-0.4508-0.0115-0.0831-0.25670.3477-0.0026-0.11310.29170.0270.48949.283328.02083.6594
77.239-5.46046.20355.8526-3.19876.5225-1.23451.8607-0.46770.3387-0.1707-0.9433-2.33721.18761.44111.1775-0.41690.11580.91830.02081.066234.183723.4567-5.4719
86.6403-4.9711-1.18414.2805-0.86466.1372-1.3127-0.78940.58250.34020.70590.49080.0373-0.30580.63780.69340.0122-0.00290.4362-0.17550.7106-8.263644.27586.9729
98.0684-5.01170.07039.9219-2.12010.6372-1.6331-1.93061.81122.03480.5864-1.37920.0304-1.2391.07721.2311-0.0118-0.23130.887-0.18891.17926.444451.35931.2173
106.5763-0.2676-1.28480.0634-0.47364.9758-0.99280.9491.0025-0.49870.64791.44650.1520.5470.44250.6958-0.0604-0.22770.43420.21110.9132-5.355853.5396-8.8421
112.8889-4.2509-2.38346.2883.8248.4951-0.51910.07582.51690.22590.19842.05230.8882-0.20750.12790.5249-0.1439-0.1570.5120.1350.9402-19.655440.4741-5.2614
126.2627-3.0856-2.35383.7844-1.12063.1630.2456-0.8762.1343-0.0894-0.52682.4738-0.4442-1.50720.55930.58520.10360.0040.7074-0.0491.6826-20.494550.8937-0.9603
135.5184.4681-0.65295.6895-2.3431.6718-0.185-0.3772.63760.46130.58091.6833-1.12380.05910.73420.79280.0344-0.70720.4301-0.34652.5089-12.828159.3118-1.7379
142.08281.52-1.60334.74570.08611.7994-0.97270.76341.1789-1.74370.62970.0639-0.7514-0.30780.18320.7336-0.1773-0.41930.76160.39951.6055-13.048950.2683-9.824
151.98511.20380.43249.2486-0.72275.151-0.52530.09561.87820.22650.3790.9454-0.56730.06370.07750.403-0.0153-0.13570.440.01920.9534-5.384750.3938-1.1233
169.71551.64081.67147.9179-1.94291.899-1.57041.92850.4227-2.45411.00671.0357-1.11690.0623-0.32661.7219-0.6205-0.80041.19640.57041.5125-10.498657.8831-17.3587
173.8124-1.3402-1.62565.19424.70769.6865-0.91820.12062.63430.91310.260.9961-0.2757-0.0060.69480.880.2278-0.22580.77180.13522.3951-16.882764.0806-3.6708
187.95523.7142-4.92574.4608-4.24524.18610.2429-0.0371-0.3860.33910.18320.1009-0.6309-0.4388-0.36550.44730.0158-0.06170.4237-0.10210.39771.767784.0503-3.8473
192.78330.69271.48583.0253-1.41871.94070.1822-0.1508-0.805-0.0850.12641.50710.1734-0.2438-0.29290.34460.04260.03370.6719-0.04110.641-7.705780.0582-8.0615
203.1341.0336-0.6646.9808-0.3090.32240.10050.4899-0.0442-0.6691-0.18380.5591-0.03570.13690.02960.3860.1193-0.0630.5062-0.17060.4622-1.395684.6023-15.0522
213.0394-1.31212.83933.2223-0.11078.33210.04770.0556-0.04890.1715-0.0308-0.35180.25880.4062-0.04340.35010.0643-0.05380.3764-0.09610.536114.92573.6888-6.6718
223.3659-1.32262.16074.4262-0.40943.2803-0.13650.21710.043-0.04850.1199-0.5109-0.00590.19910.09770.29290.02280.00910.2568-0.12090.472312.592581.9608-6.9865
233.06172.7526-0.753.0893-1.94262.71380.59020.4063-0.679-0.1761-1.2344-3.51140.85271.16050.67420.72370.201-0.11970.9437-0.07341.346228.75393.186911.1812
248.22614.41956.70894.4863.02346.9211-0.39010.1273-0.3617-2.4963-0.38430.4846-0.757-0.35480.51790.71790.2075-0.10420.8035-0.23150.582711.830766.1428-24.7018
256.0554-7.705-0.06599.934-0.04680.11970.57740.10131.10970.1865-1.1842-1.3493-0.30450.07140.52560.6896-0.132-0.13671.1244-0.35591.00728.699368.2556-21.0083
264.9742-0.3153-3.55863.2747-1.54168.69870.06531.0201-1.3079-0.0605-0.47361.00080.5674-1.10230.39470.54540.0995-0.15740.6527-0.32630.905313.169352.0946-20.8315
274.4378-1.8154-5.53236.84030.61027.60010.53120.4202-0.3327-0.6182-0.46370.43590.27450.0386-0.15370.4870.1315-0.22110.6114-0.22360.640819.983251.1388-22.2539
284.1914-4.9526-1.18197.76012.47585.16840.51331.055-0.0703-0.8214-0.42880.0710.26850.2136-0.05940.5350.1393-0.01060.5062-0.10290.400420.40461.1154-22.5435
297.7435-0.59544.12240.6893-0.92783.31920.90610.4211-1.0765-0.0958-0.81270.79030.3314-0.03810.08130.64170.2848-0.01510.7267-0.3380.786826.497845.3501-22.1288
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 266 through 283 )A266 - 283
2X-RAY DIFFRACTION2chain 'A' and (resid 284 through 297 )A284 - 297
3X-RAY DIFFRACTION3chain 'A' and (resid 298 through 320 )A298 - 320
4X-RAY DIFFRACTION4chain 'A' and (resid 321 through 329 )A321 - 329
5X-RAY DIFFRACTION5chain 'A' and (resid 330 through 416 )A330 - 416
6X-RAY DIFFRACTION6chain 'A' and (resid 417 through 454 )A417 - 454
7X-RAY DIFFRACTION7chain 'A' and (resid 455 through 465 )A455 - 465
8X-RAY DIFFRACTION8chain 'B' and (resid 762 through 771 )B762 - 771
9X-RAY DIFFRACTION9chain 'B' and (resid 772 through 781 )B772 - 781
10X-RAY DIFFRACTION10chain 'B' and (resid 782 through 789 )B782 - 789
11X-RAY DIFFRACTION11chain 'B' and (resid 790 through 799 )B790 - 799
12X-RAY DIFFRACTION12chain 'B' and (resid 800 through 813 )B800 - 813
13X-RAY DIFFRACTION13chain 'B' and (resid 814 through 825 )B814 - 825
14X-RAY DIFFRACTION14chain 'B' and (resid 826 through 840 )B826 - 840
15X-RAY DIFFRACTION15chain 'B' and (resid 841 through 866 )B841 - 866
16X-RAY DIFFRACTION16chain 'B' and (resid 867 through 878 )B867 - 878
17X-RAY DIFFRACTION17chain 'B' and (resid 879 through 888 )B879 - 888
18X-RAY DIFFRACTION18chain 'C' and (resid 268 through 292 )C268 - 292
19X-RAY DIFFRACTION19chain 'C' and (resid 293 through 307 )C293 - 307
20X-RAY DIFFRACTION20chain 'C' and (resid 308 through 339 )C308 - 339
21X-RAY DIFFRACTION21chain 'C' and (resid 340 through 416 )C340 - 416
22X-RAY DIFFRACTION22chain 'C' and (resid 417 through 453 )C417 - 453
23X-RAY DIFFRACTION23chain 'C' and (resid 454 through 465 )C454 - 465
24X-RAY DIFFRACTION24chain 'D' and (resid 762 through 771 )D762 - 771
25X-RAY DIFFRACTION25chain 'D' and (resid 772 through 781 )D772 - 781
26X-RAY DIFFRACTION26chain 'D' and (resid 782 through 813 )D782 - 813
27X-RAY DIFFRACTION27chain 'D' and (resid 814 through 840 )D814 - 840
28X-RAY DIFFRACTION28chain 'D' and (resid 841 through 866 )D841 - 866
29X-RAY DIFFRACTION29chain 'D' and (resid 867 through 888 )D867 - 888

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