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- PDB-4kfz: Crystal structure of LMO2 and anti-LMO2 VH complex -

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Basic information

Entry
Database: PDB / ID: 4kfz
TitleCrystal structure of LMO2 and anti-LMO2 VH complex
Components
  • Anti-LMO2 VH
  • LMO-2
KeywordsTRANSCRIPTION / ONCOPROTEIN / T-CELL LEUKEMIA / PROTO-ONCOGENE / DEVELOPMENTAL PROTEIN / LIM domain / transcription factor / nucleus
Function / homology
Function and homology information


bHLH transcription factor binding / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis ...bHLH transcription factor binding / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / transcription coregulator binding / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / RUNX1 regulates transcription of genes involved in differentiation of HSCs / blood microparticle / transcription regulator complex / DNA-binding transcription factor binding / Potential therapeutics for SARS / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / immune response / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / nucleoplasm / metal ion binding / identical protein binding / nucleus / plasma membrane
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. / Zinc finger, LIM-type / LIM domain profile. / : / Immunoglobulin V-Type ...: / 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. / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Ribbon / Immunoglobulin V-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy variable 3-23 / Rhombotin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSewell, H. / Tanaka, T. / El Omari, K. / Cruz-Migoni, A. / Mancini, E.J. / Fuentes-Fernandez, N. / Chambers, J. / Rabbitts, T.H.
CitationJournal: Sci Rep / Year: 2014
Title: Conformational flexibility of the oncogenic protein LMO2 primes the formation of the multi-protein transcription complex.
Authors: Sewell, H. / Tanaka, T. / Omari, K.E. / Mancini, E.J. / Cruz, A. / Fernandez-Fuentes, N. / Chambers, J. / Rabbitts, T.H.
History
DepositionApr 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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_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_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_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: LMO-2
B: LMO-2
C: Anti-LMO2 VH
D: Anti-LMO2 VH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,62112
Polymers63,0984
Non-polymers5238
Water00
1
A: LMO-2
C: Anti-LMO2 VH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8106
Polymers31,5492
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-29 kcal/mol
Surface area15900 Å2
MethodPISA
2
B: LMO-2
D: Anti-LMO2 VH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8106
Polymers31,5492
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-28 kcal/mol
Surface area16070 Å2
MethodPISA
3
A: LMO-2
C: Anti-LMO2 VH
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)190,86336
Polymers189,29312
Non-polymers1,57024
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area32110 Å2
ΔGint-200 kcal/mol
Surface area78660 Å2
MethodPISA
4
B: LMO-2
D: Anti-LMO2 VH
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)190,86336
Polymers189,29312
Non-polymers1,57024
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area33120 Å2
ΔGint-200 kcal/mol
Surface area78920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.260, 124.260, 81.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A11 - 155
2010B11 - 155
1020C3 - 127
2020D3 - 127

NCS ensembles :
ID
1
2

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Components

#1: Protein LMO-2 / Rhombotin-2 / Cysteine-rich protein TTG-2 / LIM domain only protein 2 / T-cell translocation protein 2


Mass: 17479.266 Da / Num. of mol.: 2 / Fragment: UNP residues 9-158
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMO2, RBTN2, RBTNL1, RHOM2, TTG2 / Production host: Escherichia coli (E. coli) / References: UniProt: P25791
#2: Antibody Anti-LMO2 VH


Mass: 14069.563 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Anti-LMO2 VH / Production host: Escherichia coli (E. coli) / References: UniProt: P01764*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100mM MES monohydrate pH 6.0, 0.8 M ammonium sulfate, and additive 1, 6 hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 19, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 16868 / Num. obs: 16834 / % possible obs: 99.8 % / Redundancy: 2.9 % / Net I/σ(I): 10.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UZI (chain H)

2uzi


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.909 / SU B: 32.498 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT, NON-CRYSTALLOGRAPHIC SYMMETRY (NCS) RESTRAINS WERE IMPOSED ON THE 2 VH#576/LMO2 DIMERS. TOWARDS THE END OF REFINEMENT, TLS ...Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT, NON-CRYSTALLOGRAPHIC SYMMETRY (NCS) RESTRAINS WERE IMPOSED ON THE 2 VH#576/LMO2 DIMERS. TOWARDS THE END OF REFINEMENT, TLS (TRANSLATION/LIBRATION/SCREW) VIBRATIONAL MOTION REFINEMENT WAS USED
RfactorNum. reflection% reflectionSelection details
Rfree0.25828 883 5 %RANDOM
Rwork0.23898 ---
obs0.23993 16834 99.63 %-
all-16897 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.405 Å2
Baniso -1Baniso -2Baniso -3
1--2.6 Å2-1.3 Å20 Å2
2---2.6 Å20 Å2
3---3.89 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4342 0 8 0 4350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194434
X-RAY DIFFRACTIONr_angle_refined_deg0.9041.9565986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0675544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.74423.302212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86115758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9191536
X-RAY DIFFRACTIONr_chiral_restr0.0630.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023388
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A1830.01
12B1830.01
21C1650.05
22D1650.05
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 67 -
Rwork0.319 1176 -
obs--99.92 %
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)
10.72140.0239-0.24241.5718-0.73330.4357-0.0532-0.0738-0.11470.04840.03890.0043-0.0478-0.02690.01430.2192-0.0438-0.00550.2117-0.01880.214814.3257-23.874719.0638
21.8226-0.497-0.85141.01760.01771.14140.11390.45540.0103-0.4028-0.039-0.13570.02520.18-0.07490.39960.00990.02730.5114-0.11820.05299.3963-25.93862.557
31.9917-0.99870.58772.3032-0.6872.2546-0.07080.0881-0.1015-0.07270.0534-0.2064-0.0039-0.01240.01730.1630.01-0.00120.1676-0.01420.235927.322-38.358421.5189
43.52830.24610.63554.9941.29643.91430.11190.2975-0.7014-0.2343-0.0558-0.1120.5890.2095-0.05620.43540.06640.01540.1892-0.21690.320512.7477-45.348760.1615
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 156
2X-RAY DIFFRACTION1A201 - 204
3X-RAY DIFFRACTION2B9 - 156
4X-RAY DIFFRACTION2B201 - 204
5X-RAY DIFFRACTION3C-2 - 124
6X-RAY DIFFRACTION4D-3 - 123

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