[English] 日本語
Yorodumi
- PDB-3kmp: Crystal Structure of SMAD1-MH1/DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kmp
TitleCrystal Structure of SMAD1-MH1/DNA complex
Components
  • 5'-D(P*AP*TP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*AP*TP*A)-3'
  • 5'-D(P*GP*TP*AP*TP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*A)-3'
  • SMAD1-MH1
KeywordsTRANSCRIPTION REGULATOR/DNA / protein-DNA complex / Smad1 / SBE DNA / MH1 domain / beta hairpin / Nucleus / Transcription / Transcription regulation / TRANSCRIPTION REGULATOR-DNA complex
Function / homology
Function and homology information


RUNX2 regulates bone development / mesodermal cell fate commitment / Signaling by BMP / homomeric SMAD protein complex / osteoblast fate commitment / heteromeric SMAD protein complex / co-SMAD binding / negative regulation of muscle cell differentiation / positive regulation of cartilage development / DEAD/H-box RNA helicase binding ...RUNX2 regulates bone development / mesodermal cell fate commitment / Signaling by BMP / homomeric SMAD protein complex / osteoblast fate commitment / heteromeric SMAD protein complex / co-SMAD binding / negative regulation of muscle cell differentiation / positive regulation of cartilage development / DEAD/H-box RNA helicase binding / primary miRNA binding / gamete generation / hindbrain development / SMAD protein signal transduction / embryonic pattern specification / Ub-specific processing proteases / I-SMAD binding / cartilage development / nuclear inner membrane / ureteric bud development / homeostatic process / positive regulation of sprouting angiogenesis / midbrain development / cardiac muscle cell proliferation / BMP signaling pathway / positive regulation of osteoblast differentiation / transforming growth factor beta receptor signaling pathway / male germ cell nucleus / stem cell differentiation / bone development / positive regulation of miRNA transcription / osteoblast differentiation / MAPK cascade / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / intracellular iron ion homeostasis / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / cell population proliferation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / inflammatory response / DNA-binding transcription factor activity / negative regulation of cell population proliferation / ubiquitin protein ligase binding / DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / protein kinase binding / regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / metal ion binding / identical protein binding / nucleus / cytoplasm
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 1 / MH1 domain-containing protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBaburajendran, N. / Palasingam, P. / Narasimhan, K. / Jauch, R. / Kolatkar, P.R.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Structure of Smad1 MH1/DNA complex reveals distinctive rearrangements of BMP and TGF-beta effectors.
Authors: BabuRajendran, N. / Palasingam, P. / Narasimhan, K. / Sun, W. / Prabhakar, S. / Jauch, R. / Kolatkar, P.R.
History
DepositionNov 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 11, 2013Group: Database references
Revision 1.3Mar 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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: SMAD1-MH1
B: SMAD1-MH1
C: 5'-D(P*AP*TP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*AP*TP*A)-3'
D: 5'-D(P*GP*TP*AP*TP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2538
Polymers37,9384
Non-polymers3154
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-23 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.938, 77.490, 83.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

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
11SERSERALAALAchain A resid 11:30AA11 - 303 - 22
21SERSERALAALAchain B and resid 11:30BB11 - 303 - 22
12LYSLYSCYSCYSchain A resid 32:109AA32 - 10924 - 101
22LYSLYSCYSCYSchain B and resid 32:109BB32 - 10924 - 101
13PHEPHEGLUGLUchain A resid 111:131AA111 - 131103 - 123
23PHEPHEGLUGLUchain B and resid 111:131BB111 - 131103 - 123

NCS ensembles :
ID
1
2
3

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein SMAD1-MH1


Mass: 14368.723 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 9-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smad1 / Plasmid: pETG60A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8CC31, UniProt: P70340*PLUS

-
DNA chain , 2 types, 2 molecules CD

#2: DNA chain 5'-D(P*AP*TP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*AP*TP*A)-3'


Mass: 4577.011 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(P*GP*TP*AP*TP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*A)-3'


Mass: 4624.021 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Non-polymers , 3 types, 13 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: 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: 3.16 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium tartrate dibasic, 20% PEG 3350, 10% glycerol, 3% 2-propanol (additive), vapor diffusion, hanging drop, temperature 291K

-
Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 13667 / Num. obs: 13623 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 56.33 Å2

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→23.413 Å / Occupancy max: 1 / Occupancy min: 0.46 / SU ML: 0.48 / σ(F): 1.35 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.25 683 5.01 %RANDOM
Rwork0.206 12940 --
all0.208 13667 --
obs0.208 13623 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.245 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso max: 285.28 Å2 / Biso mean: 64.761 Å2 / Biso min: 20.74 Å2
Baniso -1Baniso -2Baniso -3
1-7.724 Å2-0 Å2-0 Å2
2---4.539 Å2-0 Å2
3----3.185 Å2
Refinement stepCycle: LAST / Resolution: 2.7→23.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 617 14 9 2643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092781
X-RAY DIFFRACTIONf_angle_d1.3553876
X-RAY DIFFRACTIONf_chiral_restr0.085407
X-RAY DIFFRACTIONf_plane_restr0.006388
X-RAY DIFFRACTIONf_dihedral_angle_d20.6581103
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A164X-RAY DIFFRACTIONPOSITIONAL0.049
12B164X-RAY DIFFRACTIONPOSITIONAL0.049
21A630X-RAY DIFFRACTIONPOSITIONAL0.041
22B630X-RAY DIFFRACTIONPOSITIONAL0.041
31A181X-RAY DIFFRACTIONPOSITIONAL0.042
32B181X-RAY DIFFRACTIONPOSITIONAL0.042
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.9080.3931380.27525372675100
2.908-3.20.3081370.24525762713100
3.2-3.6620.3061560.22525422698100
3.662-4.6080.2071210.1842609273099
4.608-23.4140.1861310.1652676280798
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)
12.5468-1.1374-1.5782.5250.21730.2591-0.3086-0.1348-0.06060.49480.18620.26060.2390.07070.13090.45390.00230.06280.35840.05620.2922-6.1101-9.4663-4.7637
22.68721.2968-0.90090.9739-0.31622.01880.0913-0.30270.49570.0001-0.05260.4205-0.02040.0639-0.01460.30220.01860.05860.2753-0.10590.4423-16.891431.8765-17.0281
34.241.33462.42464.2151.41211.3401-0.2174-0.3059-0.3056-0.40810.3653-0.2543-0.6785-0.2628-0.06150.2774-0.00310.08660.3503-0.07160.2114-13.870513.6852-7.7842
42.1053-0.31011.51453.50941.59233.78510.1797-0.4447-0.5719-0.01250.1555-0.4897-0.4322-0.0561-0.44250.1331-0.0628-0.0040.37360.05970.3029-15.06498.577-8.7586
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN AA9 - 132
2X-RAY DIFFRACTION2CHAIN BB10 - 132
3X-RAY DIFFRACTION3CHAIN CC1 - 15
4X-RAY DIFFRACTION4CHAIN DD2 - 16

+
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