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- PDB-2xjy: Crystal structure of the LMO2:LDB1-LID complex, P21 crystal form -

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Basic information

Entry
Database: PDB / ID: 2xjy
TitleCrystal structure of the LMO2:LDB1-LID complex, P21 crystal form
Components
  • LIM DOMAIN-BINDING PROTEIN 1
  • RHOMBOTIN-2
KeywordsONCOPROTEIN / T-CELL LEUKEMIA / PROTO-ONCOGENE / TRANSCRIPTION / DEVELOPMENTAL PROTEIN
Function / homology
Function and homology information


Expression and translocation of olfactory receptors / regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / epithelial structure maintenance / bHLH transcription factor binding / beta-catenin-TCF complex / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery ...Expression and translocation of olfactory receptors / regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / epithelial structure maintenance / bHLH transcription factor binding / beta-catenin-TCF complex / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / LIM domain binding / gastrulation with mouth forming second / Cardiogenesis / anterior/posterior axis specification / regulation of focal adhesion assembly / cell leading edge / somatic stem cell population maintenance / positive regulation of cell adhesion / hair follicle development / regulation of cell migration / transcription coregulator binding / positive regulation of transcription elongation by RNA polymerase II / neuron differentiation / Wnt signaling pathway / Regulation of expression of SLITs and ROBOs / : / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nervous system development / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / transcription coactivator activity / cell adhesion / negative regulation of DNA-templated transcription / chromatin binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding
Similarity search - Function
LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain profile. / Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. ...LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain profile. / 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. / Ribbon / Mainly Beta
Similarity search - Domain/homology
Rhombotin-2 / LIM domain-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsEl Omari, K. / Karia, D. / Porcher, C. / Mancini, E.J.
CitationJournal: Blood / Year: 2011
Title: Structure of the Leukemia Oncogene Lmo2: Implications for the Assembly of a Hematopoietic Transcription Factor Complex.
Authors: El Omari, K. / Hoosdally, S.J. / Tuladhar, K. / Karia, D. / Vyas, P. / Patient, R. / Porcher, C. / Mancini, E.J.
History
DepositionJul 6, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1May 19, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RHOMBOTIN-2
B: LIM DOMAIN-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5346
Polymers19,2722
Non-polymers2624
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-28 kcal/mol
Surface area11080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.140, 54.360, 61.800
Angle α, β, γ (deg.)90.00, 95.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RHOMBOTIN-2 / LIM DOMAIN ONLY PROTEIN 2 / CYSTEINE-RICH PROTEIN TTG-2 / T-CELL TRANSLOCATION PROTEIN 2 / LMO-2


Mass: 15388.909 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P25791
#2: Protein/peptide LIM DOMAIN-BINDING PROTEIN 1 / NUCLEAR LIM INTERACTOR / CARBOXYL-TERMINAL LIM DOMAIN-BINDING PROTEIN 2 / LIM DOMAIN-BINDING FACTOR ...NUCLEAR LIM INTERACTOR / CARBOXYL-TERMINAL LIM DOMAIN-BINDING PROTEIN 2 / LIM DOMAIN-BINDING FACTOR CLIM2 / LDB-1 / CLIM-2 / HLDB1


Mass: 3883.274 Da / Num. of mol.: 1 / Fragment: RESIDUES 334-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q86U70
#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.: 33 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.2 % / Description: NONE
Crystal growpH: 4 / Details: 25% PEG 1500 AND 100 MM SPG, BUFFER PH 4.0

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 6395 / % possible obs: 97.8 % / Observed criterion σ(I): 1.2 / Redundancy: 3.6 % / Biso Wilson estimate: 49.18 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.3
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.2 / % possible all: 95.8

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Processing

Software
NameVersionClassification
BUSTER2.9.2refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RUT

1rut


Resolution: 2.4→40.74 Å / Cor.coef. Fo:Fc: 0.9339 / Cor.coef. Fo:Fc free: 0.9393 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 295 4.61 %RANDOM
Rwork0.2012 ---
obs0.2024 6395 --
Displacement parametersBiso mean: 63.17 Å2
Baniso -1Baniso -2Baniso -3
1--1.2233 Å20 Å22.5201 Å2
2--7.9753 Å20 Å2
3----6.752 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.4→40.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1332 0 4 33 1369
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081353HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.051812HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d498SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes37HARMONIC2
X-RAY DIFFRACTIONt_gen_planes198HARMONIC5
X-RAY DIFFRACTIONt_it1353HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.52
X-RAY DIFFRACTIONt_other_torsion17.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion163SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1376SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.68 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.265 76 4.27 %
Rwork0.2145 1704 -
all0.2167 1780 -
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)
11.3184-1.11110.01216.656-0.892-0.00970.03170.20550.0457-0.0326-0.0482-0.0562-0.0277-0.03660.0165-0.19390.0782-0.0761-0.2317-0.01670.186210.7931-9.973415.5252
22.13220.16030.45471.02590.89770.06730.01560.0238-0.05660.0021-0.01470.0423-0.053-0.0471-0.0008-0.11930.0914-0.0898-0.1906-0.0030.11320.4125-4.238513.8791
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A)
2X-RAY DIFFRACTION2(CHAIN B)

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