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- PDB-2xjz: Crystal structure of the LMO2:LDB1-LID complex, C2 crystal form -

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Basic information

Entry
Database: PDB / ID: 2xjz
TitleCrystal structure of the LMO2:LDB1-LID complex, C2 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 / MAD / Resolution: 2.8 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 1.3Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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: RHOMBOTIN-2
C: RHOMBOTIN-2
D: RHOMBOTIN-2
E: RHOMBOTIN-2
I: LIM DOMAIN-BINDING PROTEIN 1
J: LIM DOMAIN-BINDING PROTEIN 1
K: LIM DOMAIN-BINDING PROTEIN 1
L: LIM DOMAIN-BINDING PROTEIN 1
M: LIM DOMAIN-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,17532
Polymers96,79610
Non-polymers1,37922
Water1,02757
1
A: RHOMBOTIN-2
I: LIM DOMAIN-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6216
Polymers19,3592
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-61.1 kcal/mol
Surface area10480 Å2
MethodPISA
2
D: RHOMBOTIN-2
L: LIM DOMAIN-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6567
Polymers19,3592
Non-polymers2975
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-30.1 kcal/mol
Surface area10550 Å2
MethodPISA
3
E: RHOMBOTIN-2
M: LIM DOMAIN-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6216
Polymers19,3592
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-19.8 kcal/mol
Surface area10120 Å2
MethodPISA
4
B: RHOMBOTIN-2
J: LIM DOMAIN-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6567
Polymers19,3592
Non-polymers2975
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-28.1 kcal/mol
Surface area10350 Å2
MethodPISA
5
C: RHOMBOTIN-2
K: LIM DOMAIN-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6216
Polymers19,3592
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-56.6 kcal/mol
Surface area9800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.920, 55.530, 114.710
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number5
Space group name H-MC121

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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.: 5 / 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: 3970.351 Da / Num. of mol.: 5 / 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.: 20 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 5 / Details: 1.6 M NACL, 100 MM MES PH5 AND 1 MM DTT

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.28226
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28226 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 27216 / % possible obs: 96.7 % / Observed criterion σ(I): 1.8 / Redundancy: 7.3 % / Biso Wilson estimate: 80.34 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 18.8
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.8 / % possible all: 73.2

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Processing

Software
NameVersionClassification
BUSTER2.9.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.8→48.32 Å / Cor.coef. Fo:Fc: 0.8949 / Cor.coef. Fo:Fc free: 0.8872 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=6144. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=6144. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=22.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1376 5.06 %RANDOM
Rwork0.2281 ---
obs0.2289 27216 --
Displacement parametersBiso mean: 87.85 Å2
Baniso -1Baniso -2Baniso -3
1-7.96 Å20 Å24.8152 Å2
2---16.0851 Å20 Å2
3---8.1251 Å2
Refine analyzeLuzzati coordinate error obs: 0.518 Å
Refinement stepCycle: LAST / Resolution: 2.8→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6087 0 22 57 6166
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096183HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.138271HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2290SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes165HARMONIC2
X-RAY DIFFRACTIONt_gen_planes900HARMONIC5
X-RAY DIFFRACTIONt_it6183HARMONIC20
X-RAY DIFFRACTIONt_nbd8SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion18.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion740SEMIHARMONIC5
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_contact6350SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.91 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3252 110 5.32 %
Rwork0.2603 1959 -
all0.2637 2069 -
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)
13.5013-0.3135-1.37581.8276-3.02024.78440.1367-0.28160.04040.0070.04930.05560.09050.0873-0.186-0.0060.03360.0618-0.06660.0174-0.248113.958456.944129.0312
22.04240.1989-1.47574.32640.19861.3236-0.04890.2945-0.2789-0.0514-0.15620.2725-0.0164-0.41130.205-0.1181-0.03370.03130.0874-0.1087-0.1783122.388351.49566.6853
33.31571.883.50090.71570.11753.05570.0636-0.4307-0.127-0.3319-0.28990.29740.172-0.38550.2263-0.11110.0478-0.0449-0.003-0.0455-0.2757123.337938.5766-17.9807
45.242-0.26545.29243.32691.13255.25080.05860.17550.12-0.2524-0.03780.13760.06310.0962-0.02080.01030.0384-0.111-0.21490.0066-0.3024110.194941.3098-38.9718
51.9509-0.9785-1.46871.57621.23692.10190.1081-0.02880.1718-0.0233-0.32810.1962-0.0889-0.48110.2199-0.0402-0.0092-0.00460.1173-0.0591-0.244274.444350.8502-52.4882
62.1219-1.1883-0.25850-0.60463.78450.0204-0.14160.0016-0.04660.009-0.0434-0.05820.1417-0.0294-0.0455-0.08860.04790.0588-0.0588-0.054121.195553.567632.8565
70.0071-1.2584-1.85533.17950.04813.108-0.0414-0.0459-0.12670.08050.02730.1241-0.06690.07590.0141-0.10380.01240.0381-0.0064-0.09090.0177124.139344.172310.035
82.78953.84511.530.04630.8181.49330.0271-0.0951-0.0820.0009-0.03220.10030.09870.01260.00510.04350.0397-0.1460.0587-0.0823-0.0752120.105333.6776-14.3578
91.2777-5.04343.09810-1.19975.8463-0.024-0.06090.1677-0.02320.04420.0490.0943-0.1442-0.0203-0.0669-0.0458-0.0366-0.01040.0099-0.0105105.353246.51-35.7843
100.0069-3.692-1.8091.549-1.06893.12560.027-0.01770.1155-0.1077-0.01980.1365-0.16550.0303-0.0072-0.0106-0.02230.06310.0382-0.1354-0.008873.215556.686-55.9561
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A)
2X-RAY DIFFRACTION2(CHAIN B)
3X-RAY DIFFRACTION3(CHAIN C)
4X-RAY DIFFRACTION4(CHAIN D)
5X-RAY DIFFRACTION5(CHAIN E)
6X-RAY DIFFRACTION6(CHAIN I)
7X-RAY DIFFRACTION7(CHAIN J)
8X-RAY DIFFRACTION8(CHAIN K)
9X-RAY DIFFRACTION9(CHAIN L)
10X-RAY DIFFRACTION10(CHAIN M)

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