[English] 日本語
Yorodumi
- PDB-3qsv: Structural basis for DNA recognition by constitutive Smad4 MH1 dimers -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qsv
TitleStructural basis for DNA recognition by constitutive Smad4 MH1 dimers
Components
  • DNA (5'-D(P*TP*GP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*CP*A)-3')
  • Mothers against decapentaplegic homolog 4
KeywordsTRANSCRIPTION/DNA / MH1 / transcription factor / DNA binding / signaling / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


Signaling by NODAL / FOXO-mediated transcription of cell cycle genes / Signaling by Activin / RUNX3 regulates CDKN1A transcription / positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / RUNX2 regulates bone development / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis ...Signaling by NODAL / FOXO-mediated transcription of cell cycle genes / Signaling by Activin / RUNX3 regulates CDKN1A transcription / positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / RUNX2 regulates bone development / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / tissue morphogenesis / Signaling by BMP / TGF-beta receptor signaling activates SMADs / atrioventricular valve formation / activin responsive factor complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / mesendoderm development / Downregulation of SMAD2/3:SMAD4 transcriptional activity / regulation of hair follicle development / sebaceous gland development / positive regulation of luteinizing hormone secretion / filamin binding / formation of anatomical boundary / epithelial cell migration / heteromeric SMAD protein complex / positive regulation of follicle-stimulating hormone secretion / regulation of transforming growth factor beta2 production / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / neuron fate specification / cardiac septum development / secondary palate development / brainstem development / left ventricular cardiac muscle tissue morphogenesis / atrioventricular canal development / neuron fate commitment / negative regulation of cardiac muscle hypertrophy / positive regulation of extracellular matrix assembly / sulfate binding / SMAD protein signal transduction / endoderm development / Ub-specific processing proteases / outflow tract septum morphogenesis / activin receptor signaling pathway / gastrulation with mouth forming second / I-SMAD binding / cardiac muscle hypertrophy in response to stress / endothelial cell activation / neural crest cell differentiation / anterior/posterior pattern specification / adrenal gland development / branching involved in ureteric bud morphogenesis / embryonic digit morphogenesis / interleukin-6-mediated signaling pathway / ventricular septum morphogenesis / female gonad development / seminiferous tubule development / positive regulation of transforming growth factor beta receptor signaling pathway / uterus development / mesoderm development / R-SMAD binding / positive regulation of SMAD protein signal transduction / single fertilization / anatomical structure morphogenesis / developmental growth / BMP signaling pathway / positive regulation of epithelial to mesenchymal transition / ovarian follicle development / positive regulation of cardiac muscle cell apoptotic process / collagen binding / extrinsic apoptotic signaling pathway / gastrulation / ERK1 and ERK2 cascade / transforming growth factor beta receptor signaling pathway / axon guidance / transcription corepressor binding / kidney development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of canonical Wnt signaling pathway / transcription coactivator binding / cellular response to glucose stimulus / negative regulation of cell growth / negative regulation of ERK1 and ERK2 cascade / negative regulation of protein catabolic process / positive regulation of miRNA transcription / RNA polymerase II transcription regulator complex / male gonad development / osteoblast differentiation / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / in utero embryonic development / transcription by RNA polymerase II / intracellular iron ion homeostasis / cell differentiation / response to hypoxia / cell population proliferation
Similarity search - Function
Smad3; Chain A / SMAD MH1 domain / 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 ...Smad3; Chain A / SMAD MH1 domain / 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 / SMAD/FHA domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Mothers against decapentaplegic homolog 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.708 Å
AuthorsBaburajendran, N. / Jauch, R. / Zhen, C.T.Y. / Kolatkar, P.R.
CitationJournal: To be Published
Title: Structural basis for DNA recognition by constitutive Smad4 MH1 dimers
Authors: Baburajendran, N. / Jauch, R. / Zhen, C.T.Y. / Kolatkar, P.R.
History
DepositionFeb 22, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mothers against decapentaplegic homolog 4
B: Mothers against decapentaplegic homolog 4
C: Mothers against decapentaplegic homolog 4
D: Mothers against decapentaplegic homolog 4
E: DNA (5'-D(P*TP*GP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*CP*A)-3')
F: DNA (5'-D(P*TP*GP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*CP*A)-3')
G: DNA (5'-D(P*TP*GP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*CP*A)-3')
H: DNA (5'-D(P*TP*GP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,94412
Polymers79,6828
Non-polymers2624
Water1629
1
A: Mothers against decapentaplegic homolog 4
D: Mothers against decapentaplegic homolog 4
E: DNA (5'-D(P*TP*GP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*CP*A)-3')
F: DNA (5'-D(P*TP*GP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9726
Polymers39,8414
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-26 kcal/mol
Surface area17870 Å2
MethodPISA
2
B: Mothers against decapentaplegic homolog 4
C: Mothers against decapentaplegic homolog 4
G: DNA (5'-D(P*TP*GP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*CP*A)-3')
H: DNA (5'-D(P*TP*GP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9726
Polymers39,8414
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-27 kcal/mol
Surface area17790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.357, 35.354, 139.544
Angle α, β, γ (deg.)90.00, 93.83, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13E
23G
14F
24H

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROSERSERchain AAA10 - 1382 - 130
21PROPROSERSERchain BBB10 - 1382 - 130
12ASNASNVALVALchain CCC13 - 1365 - 128
22SERSERVALVALchain DDD12 - 1364 - 128
13DTDTDADAchain EEE1000 - 10151 - 16
23DTDTDADAchain GGG1000 - 10151 - 16
14DTDTDADAchain FFF2000 - 20151 - 16
24DTDTDADAchain HHH2000 - 20151 - 16

NCS ensembles :
ID
1
2
3
4

-
Components

#1: Protein
Mothers against decapentaplegic homolog 4 / Smad4


Mass: 15022.306 Da / Num. of mol.: 4 / Fragment: smad4 MH1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smad4 / Production host: Escherichia coli (E. coli) / References: UniProt: P97471
#2: DNA chain
DNA (5'-D(P*TP*GP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*CP*A)-3')


Mass: 4898.191 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA synthetically manufactured
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 200mM MgCl2, 100mM Tris, 30% PEG 4000, 10mM spermine, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 24301 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 68.38 Å2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.708→24.89 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.42 / σ(F): 0.14 / Phase error: 28.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2722 1156 5.11 %random
Rwork0.2123 ---
obs0.2153 22643 92.74 %-
all-24301 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.959 Å2 / ksol: 0.253 e/Å3
Displacement parametersBiso max: 383.88 Å2 / Biso mean: 91.1948 Å2 / Biso min: 22.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.6453 Å20 Å21.4397 Å2
2---3.5316 Å20 Å2
3---1.8863 Å2
Refinement stepCycle: LAST / Resolution: 2.708→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4076 1312 4 9 5401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045634
X-RAY DIFFRACTIONf_angle_d0.9267874
X-RAY DIFFRACTIONf_chiral_restr0.074875
X-RAY DIFFRACTIONf_plane_restr0.003771
X-RAY DIFFRACTIONf_dihedral_angle_d20.6942170
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1034X-RAY DIFFRACTIONPOSITIONAL0.029
12B1034X-RAY DIFFRACTIONPOSITIONAL0.029
21C1001X-RAY DIFFRACTIONPOSITIONAL0.015
22D1001X-RAY DIFFRACTIONPOSITIONAL0.015
31E328X-RAY DIFFRACTIONPOSITIONAL0.034
32G328X-RAY DIFFRACTIONPOSITIONAL0.034
41F328X-RAY DIFFRACTIONPOSITIONAL0.034
42H328X-RAY DIFFRACTIONPOSITIONAL0.034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7077-2.83080.39811220.31682306X-RAY DIFFRACTION82
2.8308-2.97980.35431500.28042644X-RAY DIFFRACTION92
2.9798-3.16610.29531370.22632680X-RAY DIFFRACTION94
3.1661-3.410.28671420.22722631X-RAY DIFFRACTION92
3.41-3.75210.29041530.21362784X-RAY DIFFRACTION96
3.7521-4.29270.25561380.19362738X-RAY DIFFRACTION94
4.2927-5.39920.23081590.1862704X-RAY DIFFRACTION93
5.3992-24.89150.24731550.18533000X-RAY DIFFRACTION98
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)
12.88750.6222-0.34771.11591.14495.87860.2374-0.1284-0.16770.0543-0.12380.22780.7240.1487-0.10080.442-0.05520.00520.0135-0.03380.183930.31566.5868-56.7196
22.8036-0.06270.15780.6941-0.75275.32940.0657-0.0428-0.1813-0.00570.0862-0.0944-0.6849-0.1651-0.16150.5971-0.03360.07660.1210.03480.2266-21.83422.5045-57.8606
33.30460.834-0.41372.3974-1.35770.7789-0.0386-1.3624-0.11960.47830.32530.3828-0.12-0.5291-0.29960.297-0.0870.04371.33050.31730.2384-14.668413.1366-15.3281
44.4084-1.08170.74432.78960.29280.5-0.0429-1.62470.19640.62990.3127-0.03950.1732-0.21-0.230.401-0.12570.0331.2342-0.24760.189720.868518.6758-15.4351
59.68998.1462-0.34279.67222.44295.71970.0416-2.16770.6519-0.5112-0.67450.55720.20170.24630.34960.1263-0.135-0.0030.4732-0.07290.43725.689411.9928-34.4068
69.86062.0982-1.30763.56881.27451.5692-0.6991-1.1317-1.0127-0.57720.3252-0.5559-0.11660.27620.24910.4646-0.25190.1060.3932-0.08580.441425.806311.0192-36.9435
78.43227.77580.85239.36780.70082.28360.2557-2.6934-0.884-0.6573-0.6551-0.4782-0.1068-0.2920.14740.3595-0.23340.01210.56910.19220.5705-18.59217.9284-34.8264
89.90514.73171.91136.34040.5611.1093-0.8454-1.5743-0.1554-0.93180.52790.2510.0942-0.12620.07330.4076-0.2248-0.00970.40040.07810.2818-18.601518.7881-37.4529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 10:138)A10 - 138
2X-RAY DIFFRACTION2(chain B and resid 10:138)B10 - 138
3X-RAY DIFFRACTION3(chain C and resid 13:136)C13 - 136
4X-RAY DIFFRACTION4(chain D and resid 12:136)D12 - 136
5X-RAY DIFFRACTION5(chain E and resid 1000:1015)E1000 - 1015
6X-RAY DIFFRACTION6(chain F and resid 2000:2015)F2000 - 2015
7X-RAY DIFFRACTION7(chain G and resid 1000:1015)G1000 - 1015
8X-RAY DIFFRACTION8(chain H and resid 2000:2015)H2000 - 2015

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more