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- PDB-4z9v: TCTP contains a BH3-like domain, which instead of inhibiting, act... -

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Entry
Database: PDB / ID: 4z9v
TitleTCTP contains a BH3-like domain, which instead of inhibiting, activates Bcl-xL
Components
  • Bcl-2-like protein 1,APOPTOSIS REGULATOR BCL-XL
  • Translationally-controlled tumor protein
KeywordsAPOPTOSIS / TCTP / apoptose / BH3
Function / homology
Function and homology information


negative regulation of ectoderm development / apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage ...negative regulation of ectoderm development / apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of execution phase of apoptosis / regulation of mitochondrial membrane permeability / fertilization / regulation of growth / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / cellular response to alkaloid / stem cell population maintenance / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / hepatocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of intrinsic apoptotic signaling pathway / germ cell development / apoptotic mitochondrial changes / BH3 domain binding / negative regulation of anoikis / ectopic germ cell programmed cell death / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of protein localization to plasma membrane / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ovarian follicle development / cytoplasmic microtubule / extrinsic apoptotic signaling pathway in absence of ligand / response to cytokine / multivesicular body / negative regulation of autophagy / release of cytochrome c from mitochondria / regulation of cytokinesis / epithelial cell proliferation / regulation of mitochondrial membrane potential / cellular response to amino acid stimulus / cellular response to gamma radiation / response to virus / intracellular calcium ion homeostasis / endocytosis / male gonad development / spindle pole / intrinsic apoptotic signaling pathway in response to DNA damage / RAS processing / synaptic vesicle membrane / calcium ion transport / channel activity / Interleukin-4 and Interleukin-13 signaling / spermatogenesis / regulation of apoptotic process / neuron apoptotic process / nuclear membrane / defense response to virus / DNA-binding transcription factor binding / in utero embryonic development / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / positive regulation of apoptotic process / mitochondrial matrix / calcium ion binding / centrosome / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / mitochondrion / extracellular space / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Translationally controlled tumor protein (TCTP) domain signature 1. / Translationally controlled tumour protein, conserved site / Translationally controlled tumor protein (TCTP) domain signature 2. / Translationally controlled tumour protein / Translationally controlled tumour protein (TCTP) domain / Translationally controlled tumour protein / Translationally controlled tumor protein (TCTP) domain profile. / Mss4/translationally controlled tumour-associated TCTP / Mss4-like superfamily / Apoptosis regulator, Bcl-X ...Translationally controlled tumor protein (TCTP) domain signature 1. / Translationally controlled tumour protein, conserved site / Translationally controlled tumor protein (TCTP) domain signature 2. / Translationally controlled tumour protein / Translationally controlled tumour protein (TCTP) domain / Translationally controlled tumour protein / Translationally controlled tumor protein (TCTP) domain profile. / Mss4/translationally controlled tumour-associated TCTP / Mss4-like superfamily / Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
BICARBONATE ION / Translationally-controlled tumor protein / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å
AuthorsCura, V. / Agez, M. / Thebault, S. / Cavarelli, J.
CitationJournal: Sci Rep / Year: 2016
Title: TCTP contains a BH3-like domain, which instead of inhibiting, activates Bcl-xL.
Authors: Thebault, S. / Agez, M. / Chi, X. / Stojko, J. / Cura, V. / Telerman, S.B. / Maillet, L. / Gautier, F. / Billas-Massobrio, I. / Birck, C. / Troffer-Charlier, N. / Karafin, T. / Honore, J. / ...Authors: Thebault, S. / Agez, M. / Chi, X. / Stojko, J. / Cura, V. / Telerman, S.B. / Maillet, L. / Gautier, F. / Billas-Massobrio, I. / Birck, C. / Troffer-Charlier, N. / Karafin, T. / Honore, J. / Senff-Ribeiro, A. / Montessuit, S. / Johnson, C.M. / Juin, P. / Cianferani, S. / Martinou, J.C. / Andrews, D.W. / Amson, R. / Telerman, A. / Cavarelli, J.
History
DepositionApr 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_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_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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bcl-2-like protein 1,APOPTOSIS REGULATOR BCL-XL
B: Bcl-2-like protein 1,APOPTOSIS REGULATOR BCL-XL
C: Translationally-controlled tumor protein
D: Translationally-controlled tumor protein
E: Translationally-controlled tumor protein
F: Translationally-controlled tumor protein
G: Translationally-controlled tumor protein
H: Translationally-controlled tumor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,91412
Polymers49,7468
Non-polymers1684
Water1,02757
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16280 Å2
ΔGint-143 kcal/mol
Surface area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.357, 100.357, 105.045
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11F-21-

ARG

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Components

#1: Protein Bcl-2-like protein 1,APOPTOSIS REGULATOR BCL-XL / Bcl2-L-1 / Apoptosis regulator Bcl-X


Mass: 17487.459 Da / Num. of mol.: 2
Mutation: FRAGMENT: BCL-XL DELTA-LOOP, residues 1-28 and residues 83-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Cell line (production host): pRARE2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q07817
#2: Protein/peptide
Translationally-controlled tumor protein / TCTP / Fortilin / Histamine-releasing factor / HRF / p23


Mass: 2461.807 Da / Num. of mol.: 6 / Mutation: Nterminal peptide
Source method: isolated from a genetically manipulated source
Details: TRANSLATIONALLY CONTROLLED TUMOR PROTEIN; N terminal Fragment 11-31
Source: (gene. exp.) Homo sapiens (human) / Gene: TPT1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P13693
#3: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.5M Tris-sodium citrate, 100mM Pipes pH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.099→46.535 Å / Num. obs: 31973 / % possible obs: 99.7 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 19.2
Reflection shellResolution: 2.099→2.23 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 1.1 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIXdev_1702refinement
XDSdata reduction
HKL-2000data reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P1L

2p1l


Resolution: 2.099→46.535 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0.12 / Phase error: 27.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 2995 5.01 %Random selection
Rwork0.1851 ---
obs0.187 31874 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.099→46.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3369 0 10 57 3436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033448
X-RAY DIFFRACTIONf_angle_d0.7694640
X-RAY DIFFRACTIONf_dihedral_angle_d14.4281251
X-RAY DIFFRACTIONf_chiral_restr0.028492
X-RAY DIFFRACTIONf_plane_restr0.003601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0988-2.13320.39481350.35872532X-RAY DIFFRACTION94
2.1332-2.170.34891440.33872696X-RAY DIFFRACTION100
2.17-2.20950.36081430.31922701X-RAY DIFFRACTION100
2.2095-2.2520.34291380.30482701X-RAY DIFFRACTION100
2.252-2.29790.3871440.28322719X-RAY DIFFRACTION100
2.2979-2.34790.27451480.26722705X-RAY DIFFRACTION100
2.3479-2.40250.3321440.26112704X-RAY DIFFRACTION100
2.4025-2.46260.31451420.24532724X-RAY DIFFRACTION100
2.4626-2.52920.27141400.24372719X-RAY DIFFRACTION100
2.5292-2.60360.26621460.24352696X-RAY DIFFRACTION100
2.6036-2.68760.27081410.24212711X-RAY DIFFRACTION100
2.6876-2.78360.26871490.22582719X-RAY DIFFRACTION100
2.7836-2.89510.22981430.21632701X-RAY DIFFRACTION100
2.8951-3.02680.27511470.22182710X-RAY DIFFRACTION100
3.0268-3.18640.2261390.21062703X-RAY DIFFRACTION100
3.1864-3.38590.30321400.20542727X-RAY DIFFRACTION100
3.3859-3.64730.18951440.17492693X-RAY DIFFRACTION100
3.6473-4.01410.17741470.14652724X-RAY DIFFRACTION100
4.0141-4.59460.17261390.13552718X-RAY DIFFRACTION100
4.5946-5.78690.17021400.14962706X-RAY DIFFRACTION100
5.7869-46.54620.20091420.15822717X-RAY DIFFRACTION100
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)
15.89140.5822.34864.1381-3.66847.1996-0.0038-0.150.3628-0.06930.1371-0.0333-0.00930.0357-0.12750.39680.03950.05260.3756-0.00720.413233.156732.041132.5739
25.52393.22192.53779.11663.58866.7873-0.47860.501-0.3164-1.14720.10850.32530.13230.0750.37320.7090.07630.10520.36270.00610.475421.103514.067221.433
36.0132-5.17051.99464.295-2.0324.0427-0.09490.1649-1.0619-0.07330.14250.95450.5057-0.6146-0.1430.5286-0.02330.03120.48130.00260.69167.0598.984230.9467
46.8935-1.0621-0.13723.9799-0.55762.2042-0.05690.1324-0.24-0.0649-0.0486-0.29140.31790.0940.05480.47680.00980.04840.32960.02110.434219.28113.806230.187
55.0152.8118-3.34913.0103-1.51753.7226-0.3202-0.1958-0.0196-0.309-0.0048-0.25350.26170.41780.28490.47390.11280.04920.37560.01630.449428.243327.81924.256
63.0342-0.04881.46562.7185-1.09637.1919-0.05180.28550.526-0.04060.0581-0.2831-0.44510.56130.02310.4041-0.01960.10550.42940.03230.588738.363839.675324.5266
71.68393.25090.61656.69-0.27945.6795-0.61840.436-1.2405-0.79960.3383-0.0408-0.1612-0.09460.04070.82350.0510.03910.4174-0.06490.655517.46122.779623.0516
84.22683.9165.63199.39983.27279.92620.04621.0660.98340.25690.3788-0.395-0.09671.3561-0.13730.5396-0.00230.1670.82390.06320.652544.933439.721514.5875
96.8274-6.6538-6.37847.03346.7986.60060.50410.59330.213-1.161-0.48230.7582-1.3816-1.0618-0.46290.77750.14-0.02550.84510.10661.06615.47835.8822.7314
103.809-3.59121.24923.666-0.33796.6236-0.0575-1.20130.50111.0560.24761.1254-0.1072-1.107-0.23790.63310.02320.15410.5999-0.06270.77787.37332.5835.1115
119.78540.2572.08549.10985.61433.85480.47690.0575-0.0943-0.0191-0.2071-0.97911.5514-0.1345-0.28880.69730.0801-0.0040.83510.04150.647143.500523.605744.7218
127.33390.44843.30962.1768-1.23332.50910.1517-0.45310.30480.0388-0.81030.1615-0.8181-0.21860.41370.52950.0094-0.00490.6864-0.07980.673836.904933.762246.3433
135.96836.7291-5.17077.872-6.15464.88750.9115-0.04872.57230.5281-0.17581.6604-1.18360.2281-0.82690.56670.04310.07360.5368-0.04461.019816.687141.189532.345
142.175-0.8767-2.01932.1686-0.98277.6014-0.3582-1.17750.59370.49380.28210.2073-1.4888-0.3633-0.00950.7260.16030.06440.70120.01150.663214.914831.203334.6694
158.87133.00764.48012.29652.47049.36720.2773-1.7459-0.14060.3679-0.44890.59481.2633-0.73320.19860.6378-0.03980.06890.9542-0.00570.624327.733524.471346.0106
169.5215-2.64721.7867.6342-3.64918.5551-0.7612-1.11490.54491.20170.7155-0.5012-0.544-0.43120.08470.70490.049-0.07110.6498-0.06560.634330.944532.639740.3264
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 111 )
3X-RAY DIFFRACTION3chain 'A' and (resid 112 through 136 )
4X-RAY DIFFRACTION4chain 'A' and (resid 137 through 208 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 110 )
6X-RAY DIFFRACTION6chain 'B' and (resid 111 through 207 )
7X-RAY DIFFRACTION7chain 'C' and (resid 15 through 29 )
8X-RAY DIFFRACTION8chain 'D' and (resid 14 through 29 )
9X-RAY DIFFRACTION9chain 'E' and (resid 11 through 19 )
10X-RAY DIFFRACTION10chain 'E' and (resid 20 through 31 )
11X-RAY DIFFRACTION11chain 'F' and (resid 11 through 19 )
12X-RAY DIFFRACTION12chain 'F' and (resid 20 through 30 )
13X-RAY DIFFRACTION13chain 'G' and (resid 11 through 23 )
14X-RAY DIFFRACTION14chain 'G' and (resid 24 through 31 )
15X-RAY DIFFRACTION15chain 'H' and (resid 11 through 23 )
16X-RAY DIFFRACTION16chain 'H' and (resid 24 through 31 )

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