[English] 日本語
Yorodumi
- PDB-3mmk: The structural basis for partial redundancy in a class of transcr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mmk
TitleThe structural basis for partial redundancy in a class of transcription factors, the lim-homeodomain proteins, in neural cell type specification
ComponentsFusion of LIM/homeobox protein Lhx4, linker, Insulin gene enhancer protein ISL-2
KeywordsMETAL BINDING PROTEIN / Protein-protein complex / LIM domain / Zn finger / DNA-binding / Homeobox / Metal-binding / Nucleus / Transcription / Transcriptional regulation
Function / homology
Function and homology information


visceral motor neuron differentiation / medial motor column neuron differentiation / spinal cord motor neuron cell fate specification / neuron fate specification / neuron fate commitment / methyl-CpG binding / motor neuron axon guidance / retinal ganglion cell axon guidance / negative regulation of neuron differentiation / cis-regulatory region sequence-specific DNA binding ...visceral motor neuron differentiation / medial motor column neuron differentiation / spinal cord motor neuron cell fate specification / neuron fate specification / neuron fate commitment / methyl-CpG binding / motor neuron axon guidance / retinal ganglion cell axon guidance / negative regulation of neuron differentiation / cis-regulatory region sequence-specific DNA binding / axonogenesis / animal organ morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / placenta development / neuron differentiation / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of apoptotic process / regulation of transcription by RNA polymerase II / apoptotic process / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
: / : / : / : / : / Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. ...: / : / : / : / : / Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
LIM/homeobox protein Lhx4 / Insulin gene enhancer protein ISL-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.157 Å
AuthorsGadd, M.S. / Langley, D.B. / Guss, J.M. / Matthews, J.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The structural basis for partial redundancy in a class of transcription factors, the lim-homeodomain proteins, in neural cell type specification.
Authors: Gadd, M.S. / Bhati, M. / Jeffries, C.M. / Langley, D.B. / Trewhella, J. / Guss, J.M. / Matthews, J.M.
History
DepositionApr 20, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references / Structure summary
Revision 1.2Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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: Fusion of LIM/homeobox protein Lhx4, linker, Insulin gene enhancer protein ISL-2
B: Fusion of LIM/homeobox protein Lhx4, linker, Insulin gene enhancer protein ISL-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,96414
Polymers37,2992
Non-polymers66512
Water55831
1
A: Fusion of LIM/homeobox protein Lhx4, linker, Insulin gene enhancer protein ISL-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0178
Polymers18,6491
Non-polymers3687
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fusion of LIM/homeobox protein Lhx4, linker, Insulin gene enhancer protein ISL-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9466
Polymers18,6491
Non-polymers2975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.823, 88.734, 49.851
Angle α, β, γ (deg.)90.00, 111.85, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Fusion of LIM/homeobox protein Lhx4, linker, Insulin gene enhancer protein ISL-2 / LIM homeobox protein 4


Mass: 18649.264 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 24-149 AND 272-301
Source method: isolated from a genetically manipulated source
Details: Fusion of Lhx4 residues 24-149 to Isl2 residues 272-301 via a glycine rich linker with sequence GGSGGHMGSGG
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsh-4, Gsh4, Isl2, Lhx4 / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P53776, UniProt: Q9CXV0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFUSION OF LHX4 RESIDUES 24-149 TO ISL2 RESIDUES 272-301 VIA A GLYCINE RICH LINKER WITH SEQUENCE GGSGGHMGSGG

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.27 % / Description: The file contains Friedel pairs.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.5M magnesium sulphate, 0.1M MES, 3% (w/v) sucrose, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.2819 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2819 Å / Relative weight: 1
ReflectionResolution: 2.157→50 Å / Num. all: 20403 / Num. obs: 20403 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 52.61 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 14.269
Reflection shellResolution: 2.16→2.2 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.458 / Rsym value: 0.473 / % possible all: 78.2

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.157→23.135 Å / SU ML: 0.41 / Isotropic thermal model: Isotropic / σ(F): 1.9 / Phase error: 32.04 / Stereochemistry target values: ML / Details: The file contains Friedel pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.2651 2022 5.16 %Random
Rwork0.2348 ---
obs0.2366 20403 97.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.962 Å2 / ksol: 0.409 e/Å3
Displacement parametersBiso mean: 57.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.8478 Å20 Å2-6.3283 Å2
2---11.0396 Å20 Å2
3---5.1918 Å2
Refinement stepCycle: LAST / Resolution: 2.157→23.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 0 12 31 2236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032239
X-RAY DIFFRACTIONf_angle_d0.6553044
X-RAY DIFFRACTIONf_dihedral_angle_d13.402730
X-RAY DIFFRACTIONf_chiral_restr0.048344
X-RAY DIFFRACTIONf_plane_restr0.002400
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1572-2.21110.3137920.2938231585
2.2111-2.27080.3851280.3042259995
2.2708-2.33760.31091440.2976266398
2.3376-2.41290.32231750.26922644100
2.4129-2.49910.28231470.274272699
2.4991-2.5990.31991390.24692754100
2.599-2.71710.30321320.26672668100
2.7171-2.86010.26891420.27732738100
2.8601-3.03890.29741760.25642671100
3.0389-3.2730.32051300.2682719100
3.273-3.60130.32381530.2093272599
3.6013-4.11980.19981440.1937266899
4.1198-5.18090.19411380.1749269198
5.1809-23.13620.21911820.2208258897
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)
10.25240.4456-0.420.65820.2291-0.0790.12130.11390.3795-0.17990.14330.00580.33510.2017-0.00010.50540.0325-0.15730.4533-0.06430.542836.311681.250541.2282
20.06890.4065-0.3107-0.00440.02540.1697-0.3959-0.09650.1814-0.07750.1777-0.09460.61730.2711-0.00020.7254-0.0483-0.19080.4858-0.04310.523731.268172.476529.4301
30.6168-0.4263-1.16711.83831.61572.08950.0327-0.0519-0.167-0.35030.07910.1377-0.59410.19860.00010.4-0.0668-0.06110.40520.00890.344715.46253.731334.4046
40.1090.7194-0.78810.1282-0.00660.14370.1032-0.24070.85740.34110.49480.50210.6481-0.4869-0.00620.4832-0.0159-0.00910.6215-0.19670.732226.517880.318342.6891
50.09740.81230.00830.67750.9743-0.30650.21480.1038-0.04910.0874-0.01980.0915-0.34350.27540.00010.5237-0.00150.12490.3821-0.03720.532510.961923.373455.5941
60.97291.11580.36250.49280.55471.4096-0.01740.03540.17410.1650.02980.11650.50080.01590.00040.36360.04270.05210.3505-0.02050.3262-7.620447.680958.7592
7-0.3775-0.48620.31580.2737-0.62390.32950.14880.38580.1933-0.40650.141-0.0244-0.3105-0.58340.00010.61340.1189-0.00530.6437-0.08660.53574.10119.212647.1196
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 26:61)
2X-RAY DIFFRACTION2(chain A and resid 62:86)
3X-RAY DIFFRACTION3(chain A and resid 87:286)
4X-RAY DIFFRACTION4(chain A and resid 287:299)
5X-RAY DIFFRACTION5(chain B and resid 26:85)
6X-RAY DIFFRACTION6(chain B and resid 86:285)
7X-RAY DIFFRACTION7(chain B and resid 286:301)

+
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