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- PDB-4pl7: Structure of Komagataella pastoris actin-thymosin beta4 hybrid -

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Basic information

Entry
Database: PDB / ID: 4pl7
TitleStructure of Komagataella pastoris actin-thymosin beta4 hybrid
ComponentsActin,Thymosin beta-4
KeywordsSTRUCTURAL PROTEIN / CONTRACTILE PROTEIN
Function / homology
Function and homology information


positive regulation of proton-transporting ATP synthase activity, rotational mechanism / sequestering of actin monomers / positive regulation of endothelial cell chemotaxis / positive regulation of ATP biosynthetic process / actin monomer binding / positive regulation of blood vessel endothelial cell migration / negative regulation of canonical NF-kappaB signal transduction / regulation of cell migration / tumor necrosis factor-mediated signaling pathway / protein sequestering activity ...positive regulation of proton-transporting ATP synthase activity, rotational mechanism / sequestering of actin monomers / positive regulation of endothelial cell chemotaxis / positive regulation of ATP biosynthetic process / actin monomer binding / positive regulation of blood vessel endothelial cell migration / negative regulation of canonical NF-kappaB signal transduction / regulation of cell migration / tumor necrosis factor-mediated signaling pathway / protein sequestering activity / platelet alpha granule lumen / actin filament organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / negative regulation of inflammatory response / Platelet degranulation / cytoskeleton / hydrolase activity / enzyme binding / RNA binding / extracellular region / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Thymosin beta-4 family signature. / Beta-thymosin / Beta-thymosin superfamily / Thymosin beta-4 family / Thymosin beta actin-binding motif. / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site ...Thymosin beta-4 family signature. / Beta-thymosin / Beta-thymosin superfamily / Thymosin beta-4 family / Thymosin beta actin-binding motif. / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Thymosin beta-4 / Actin
Similarity search - Component
Biological speciesKomagataella pastoris (fungus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsXue, B. / Robinson, R.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis of thymosin-beta 4/profilin exchange leading to actin filament polymerization.
Authors: Xue, B. / Leyrat, C. / Grimes, J.M. / Robinson, R.C.
History
DepositionMay 16, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / software / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin,Thymosin beta-4
B: Actin,Thymosin beta-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0606
Polymers96,9652
Non-polymers1,0954
Water4,089227
1
A: Actin,Thymosin beta-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0303
Polymers48,4831
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Actin,Thymosin beta-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0303
Polymers48,4831
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.508, 139.495, 56.485
Angle α, β, γ (deg.)90.000, 116.210, 90.000
Int Tables number4
Space group name H-MP1211
Detailsmonomer

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Components

#1: Protein Actin,Thymosin beta-4 / T beta-4 / Fx


Mass: 48482.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella pastoris (fungus), (gene. exp.) Homo sapiens (human)
Strain: GS115 / ATCC 20864 / Gene: ACT1, PAS_chr3_1169, TMSB4X, TB4X, THYB4, TMSB4 / Plasmid: pPICZc, modified / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: Q9P4D1, UniProt: P62328
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.06 Å3/Da / Density % sol: 40.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M sodium acetate, 15% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2009 / Details: Quantum-315
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 37614 / % possible obs: 94.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.109 / Χ2: 0.897 / Net I/av σ(I): 10.295 / Net I/σ(I): 10.6 / Num. measured all: 132268
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.282.80.37328470.931171.8
2.28-2.3730.32832940.9682.8
2.37-2.483.20.31937000.96893.1
2.48-2.613.50.27939110.94398.6
2.61-2.773.70.22339181.01199.7
2.77-2.983.70.17240181.0199.9
2.98-3.283.70.13239780.94199.9
3.28-3.763.70.10539760.881100
3.76-4.723.70.09339820.79899.9
4.72-203.70.0839900.5999.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
DENZOdata collection
SCALEPACKdata reduction
PHASER2.5.5phasing
PDB_EXTRACT3.11data extraction
Cootmodel building
PHASERmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YAG, chain A

1yag


Resolution: 2.3→19.831 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 28.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2579 1477 5.05 %Random selection
Rwork0.195 27796 --
obs0.1982 29273 84.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.22 Å2 / Biso mean: 34.1052 Å2 / Biso min: 7.43 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5976 0 64 227 6267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136176
X-RAY DIFFRACTIONf_angle_d1.3228348
X-RAY DIFFRACTIONf_chiral_restr0.053931
X-RAY DIFFRACTIONf_plane_restr0.0081063
X-RAY DIFFRACTIONf_dihedral_angle_d15.9642308
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.38210.3244900.26441780187054
2.3821-2.47730.3701970.26982016211361
2.4773-2.58980.32941050.26282226233167
2.5898-2.7260.33441110.25272495260676
2.726-2.89630.30231600.23312881304188
2.8963-3.11920.29521950.22693245344098
3.1192-3.43160.28871680.202732743442100
3.4316-3.92480.23861750.175733053480100
3.9248-4.93230.20951710.151833003471100
4.9323-19.83180.21652050.16813274347999
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)
10.0108-0.01080.00230.03660.03260.0322-0.1398-0.0987-0.28830.1329-0.11050.6516-0.095-0.214900.22820.01440.05710.248-0.02020.2896-9.701-12.918725.4809
20.069-0.0643-0.01530.02310.03810.060.4079-0.5280.04210.0418-0.040.1343-0.4659-0.094500.44470.2745-0.0572-5.60092.0417-0.4716-4.2738-11.499716.7678
30.44340.08390.01130.25050.34860.2946-0.04550.76110.21640.30250.34720.2878-0.7715-0.63700.48470.1517-0.0670.3027-0.02460.3372-9.9393-8.04056.3622
40.2593-0.35210.22860.6419-0.05990.5824-0.3070.51590.2265-0.23610.1228-0.0829-1.1487-1.121600.67490.1070.03360.1476-0.01830.2144-8.3214-3.824817.4231
5-0.01360.0362-0.02370.0031-0.0317-0.01560.0574-0.23230.69110.2318-0.1194-0.3647-0.13920.5019-00.77780.41050.2889-2.35-2.672-1.9176-0.25475.004223.6988
60.44770.51550.31960.38320.27080.54940.086-0.4476-0.0670.3514-0.17570.0804-0.9270.5594-00.5102-0.02520.06130.0388-0.04490.19131.8337-7.15423.524
7-00.0087-0.05430.06010.05910.0595-0.2653-1.17270.4380.24910.10070.2126-0.5323-0.019-00.7299-0.2459-0.0080.4749-0.06280.312515.9542-5.106325.2513
80.32890.11530.17710.2571-0.36360.16420.3283-0.0666-0.0604-0.28980.0601-0.3134-0.9254-0.021200.4066-0.0735-0.00420.34530.00570.24810.3253-7.4383-3.4673
90.28810.2102-0.14720.18220.06330.3392-0.04220.44510.0908-0.2178-0.29340.034-0.199-0.3172-00.2645-0.00370.03330.2508-0.01680.21735.1101-13.6824-4.2982
100.0143-0.0349-0.00170.0099-0.00120.00790.1931-0.089-0.4722-0.5352-0.36960.09370.69330.3088-0-2.51270.04550.64571.025-0.08950.370425.0715-19.9542-5.2705
110.00220.0014-0.0207-0.00910.0041-0.0002-0.0797-0.19580.131-0.2226-0.0509-0.3426-0.03950.073200.3663-0.03690.07750.55940.07550.44719.4678-25.5239-12.1885
120.01760.0057-0.020.06410.04250.0361-0.10620.50750.0633-0.5071-0.48730.11490.1562-0.20900.35680.0269-0.05590.321-0.1560.41312.2549-20.7956-11.9448
130.285-0.2293-0.11610.2657-0.34030.2872-0.20690.24710.488-0.8275-0.5805-0.1695-1.34890.422300.2671-0.18740.03420.48790.12870.270217.7813-10.2456-0.9202
140.24960.04710.12850.0961-0.18590.1172-0.7507-0.8213-0.24320.80530.0289-0.28950.7561.862100.1081-0.3941-0.23920.5790.11040.229622.6947-13.989717.0411
150.0089-0.0326-0.04610.0690.01050.0310.0645-0.281-0.50590.3381-0.30760.0186-0.01450.434200.3261-0.0169-0.10630.06710.05240.32679.9061-19.902516.7008
16-0.1831-0.0653-0.16140.1191-0.15010.15030.3646-2.1203-0.42210.21820.0032-0.1458-0.6969-0.424100.52860.05930.09250.213-0.15220.1796-4.7238-7.805733.4312
170.0813-0.1282-0.10930.12420.00820.0903-0.2059-0.21830.01960.42450.0269-0.4230.26990.5334-00.6114-0.1130.03910.40850.16370.38573.9108-22.40731.8883
180.02470.0574-0.01030.03080.02740.0490.09390.0229-0.2313-0.40720.0204-0.0707-0.09780.225700.3923-0.3172-0.2415-0.641-0.18970.5104-7.0002-22.945413.9719
190.04210.02460.00490.0238-0.00750.00260.0379-0.1127-0.1586-0.2041-0.2290.08740.082-0.171900.3744-0.01930.03270.45670.03870.2343-8.2282-14.0711-2.4433
200.0153-0.01920.00170.00620.0210.01370.23110.14040.4486-0.3150.1869-0.0547-0.2580.0014-00.4290.1263-0.14640.7332-0.05610.5039-9.2825-5.6879-12.1495
210.3610.45310.1070.17270.01050.32960.0823-0.1551-0.06820.1529-0.0057-0.0313-0.1037-0.061200.21070.01970.01450.19970.01220.227211.227527.14334.2732
220.0265-0.0244-0.00420.0353-0.04010.1028-0.1123-0.3194-0.06670.6095-0.06070.06820.5082-0.038300.367-0.0149-0.07680.59840.09360.507422.585418.966516.0838
230.0228-0.01440.03070.06760.00190.07770.5442-1.2886-0.83980.10240.31690.01350.65690.2564-00.43850.0019-0.2024-0.18670.17250.618116.399212.37233.8
240.70050.19540.40010.6896-0.55180.35390.0483-0.3535-0.1690.35190.31380.05350.57430.0024-00.1821-0.04220.00040.41620.15820.34486.157821.87656.9054
250.0182-0.0278-0.04040.02170.0138-0.0133-0.25070.364-0.2161-0.3765-0.0231-0.01520.2951-0.2946-00.5108-0.1601-0.16630.31630.10880.5857.54799.491-4.0638
260.7357-0.09220.3050.75550.93450.70410.56870.6285-0.42260.02640.22970.23660.0094-0.6853-00.1675-0.0793-0.06950.05770.08950.35859.194621.7961-7.8249
27-0.00640.1437-0.02250.1061-0.04380.08550.38450.2911-0.46620.1906-0.22430.33710.7273-0.5322-00.3820.0818-0.15530.3484-0.16960.654917.687417.2702-16.2066
280.0477-0.15930.11070.1156-0.02420.21390.1742-0.3951-0.80170.47620.0155-0.39630.25190.0628-00.22930.0836-0.04190.2693-0.05390.297538.853322.7905-0.1851
290.58450.25270.23570.36860.32290.27320.4577-0.0338-0.3099-0.3691-0.2881-0.0680.5780.719200.14120.0356-0.02410.3351-0.07450.281836.047328.56890.7316
300.00230.01270.02750.0148-0.0014-0.02260.01390.39110.40920.2168-0.18130.1912-0.5427-0.389600.4260.00520.03330.52070.16440.565648.016836.5835-11.7985
310.2034-0.03560.10720.06370.09650.0567-0.17710.1034-0.4390.2907-0.336-0.9824-0.23680.465500.3366-0.1117-0.02860.4469-0.12360.367141.619736.19756.708
320.3305-0.2392-0.12060.1896-0.31410.30110.4921-0.1446-1.3980.7847-0.5393-1.2806-0.2370.72270-0.09670.31420.19310.254-0.2610.298537.751824.6071-9.7757
330.02740.04360.02080.04470.08020.09770.41041.08560.1917-0.75010.62340.54640.2326-0.977100.33260.1212-0.02590.2899-0.38490.194620.863523.0669-25.9052
340.1265-0.0649-0.14310.0127-0.19440.1218-0.07930.59160.1289-1.38350.2120.5343-0.93561.10070-0.41660.30460.11120.2617-0.09760.259226.061431.4688-17.5996
350.27530.11120.0760.1599-0.04320.00730.21041.87580.1698-0.24330.01770.1653-0.4809-0.112500.46240.09330.0655-0.46180.04860.258319.804234.4161-15.9528
360.121-0.06290.23060.2427-0.0082-0.05640.4172-0.1586-0.659-0.05590.10310.021.0123-2.9533-0-0.82060.35660.05210.19320.02010.444-2.414523.0178-4.5203
370.16180.0234-0.00410.0586-0.11030.06730.00980.92520.2994-0.2593-0.09880.4542-0.2897-0.4981-00.42840.10670.06480.27570.10590.54452.161836.7733-11.7934
380.0405-0.0181-0.0102-0.00080.02330.03330.03310.06750.32050.4052-0.0346-0.3534-0.38820.0486-00.3366-0.00490.09430.3313-0.06250.423713.611637.56345.7811
390.01630.0036-0.00730.0193-0.0130.016-0.1169-0.0392-0.0891-0.0386-0.1312-0.2415-0.16860.007400.1540.0201-0.0260.6487-0.0240.204229.742127.384515.8741
400.0039-0.0044-0.00570.0032-0.01010.0089-0.36220.1274-0.2762-0.0894-0.0716-0.18440.04070.072600.43260.01040.00430.6107-0.02950.438736.83318.082919.4791
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 5:10)A5 - 10
2X-RAY DIFFRACTION2(chain A and resid 11:23)A11 - 23
3X-RAY DIFFRACTION3(chain A and resid 24:68)A24 - 68
4X-RAY DIFFRACTION4(chain A and resid 69:110)A69 - 110
5X-RAY DIFFRACTION5(chain A and resid 111:119)A111 - 119
6X-RAY DIFFRACTION6(chain A and resid 120:161)A120 - 161
7X-RAY DIFFRACTION7(chain A and resid 162:177)A162 - 177
8X-RAY DIFFRACTION8(chain A and resid 178:197)A178 - 197
9X-RAY DIFFRACTION9(chain A and resid 198:221)A198 - 221
10X-RAY DIFFRACTION10(chain A and resid 222:230)A222 - 230
11X-RAY DIFFRACTION11(chain A and resid 231:236)A231 - 236
12X-RAY DIFFRACTION12(chain A and resid 237:249)A237 - 249
13X-RAY DIFFRACTION13(chain A and resid 250:272)A250 - 272
14X-RAY DIFFRACTION14(chain A and resid 273:326)A273 - 326
15X-RAY DIFFRACTION15(chain A and resid 327:339)A327 - 339
16X-RAY DIFFRACTION16(chain A and resid 340:365)A340 - 365
17X-RAY DIFFRACTION17(chain A and resid 394:407)A394 - 407
18X-RAY DIFFRACTION18(chain A and resid 408:413)A408 - 413
19X-RAY DIFFRACTION19(chain A and resid 414:420)A414 - 420
20X-RAY DIFFRACTION20(chain A and resid 421:429)A421 - 429
21X-RAY DIFFRACTION21(chain B and resid 5:36)B5 - 36
22X-RAY DIFFRACTION22(chain B and resid 52:68)B52 - 68
23X-RAY DIFFRACTION23(chain B and resid 69:83)B69 - 83
24X-RAY DIFFRACTION24(chain B and resid 84:110)B84 - 110
25X-RAY DIFFRACTION25(chain B and resid 111:119)B111 - 119
26X-RAY DIFFRACTION26(chain B and resid 120:167)B120 - 167
27X-RAY DIFFRACTION27(chain B and resid 168:181)B168 - 181
28X-RAY DIFFRACTION28(chain B and resid 182:197)B182 - 197
29X-RAY DIFFRACTION29(chain B and resid 198:224)B198 - 224
30X-RAY DIFFRACTION30(chain B and resid 225:233)B225 - 233
31X-RAY DIFFRACTION31(chain B and resid 234:249)B234 - 249
32X-RAY DIFFRACTION32(chain B and resid 250:272)B250 - 272
33X-RAY DIFFRACTION33(chain B and resid 273:293)B273 - 293
34X-RAY DIFFRACTION34(chain B and resid 294:322)B294 - 322
35X-RAY DIFFRACTION35(chain B and resid 323:338)B323 - 338
36X-RAY DIFFRACTION36(chain B and resid 339:364)B339 - 364
37X-RAY DIFFRACTION37(chain B and resid 394:407)B394 - 407
38X-RAY DIFFRACTION38(chain B and resid 408:413)B408 - 413
39X-RAY DIFFRACTION39(chain B and resid 414:423)B414 - 423
40X-RAY DIFFRACTION40(chain B and resid 424:429)B424 - 429

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