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- PDB-6gjh: Human Hsp27 (HspB1) alpha-crystallin domain in complex with a pep... -

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Basic information

Entry
Database: PDB / ID: 6gjh
TitleHuman Hsp27 (HspB1) alpha-crystallin domain in complex with a peptide mimic of its phosphorylatable N-terminal region
Components
  • ALA-LEU-SER-ARG
  • ALA-LEU-SER-ARG-GLN
  • Heat shock protein beta-1Heat shock response
  • LEU-SER-GLY-VAL
KeywordsCHAPERONE / Ig-fold / sHSP
Function / homology
Function and homology information


anterograde axonal protein transport / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cornified envelope / positive regulation of endothelial cell chemotaxis / regulation of translational initiation / regulation of canonical NF-kappaB signal transduction / protein kinase C inhibitor activity / response to unfolded protein / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus ...anterograde axonal protein transport / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cornified envelope / positive regulation of endothelial cell chemotaxis / regulation of translational initiation / regulation of canonical NF-kappaB signal transduction / protein kinase C inhibitor activity / response to unfolded protein / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / chaperone-mediated protein folding / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein folding chaperone / axon cytoplasm / proteasome complex / protein kinase C binding / ubiquitin binding / positive regulation of interleukin-1 beta production / regulation of autophagy / AUF1 (hnRNP D0) binds and destabilizes mRNA / regulation of protein phosphorylation / negative regulation of protein kinase activity / MAPK6/MAPK4 signaling / response to virus / spindle / platelet aggregation / Z disc / VEGFA-VEGFR2 Pathway / positive regulation of angiogenesis / unfolded protein binding / positive regulation of tumor necrosis factor production / response to heat / protein refolding / RNA polymerase II-specific DNA-binding transcription factor binding / Extra-nuclear estrogen signaling / cytoskeleton / intracellular signal transduction / focal adhesion / negative regulation of apoptotic process / protein kinase binding / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Heat shock protein beta-1, ACD domain / Alpha crystallin/Small heat shock protein, animal type / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone
Similarity search - Domain/homology
Heat shock protein beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsCollier, M.P. / Benesch, J.L.P.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K004247/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J018082/1 United Kingdom
CitationJournal: Sci Adv / Year: 2019
Title: HspB1 phosphorylation regulates its intramolecular dynamics and mechanosensitive molecular chaperone interaction with filamin C.
Authors: Collier, M.P. / Alderson, T.R. / de Villiers, C.P. / Nicholls, D. / Gastall, H.Y. / Allison, T.M. / Degiacomi, M.T. / Jiang, H. / Mlynek, G. / Furst, D.O. / van der Ven, P.F.M. / Djinovic- ...Authors: Collier, M.P. / Alderson, T.R. / de Villiers, C.P. / Nicholls, D. / Gastall, H.Y. / Allison, T.M. / Degiacomi, M.T. / Jiang, H. / Mlynek, G. / Furst, D.O. / van der Ven, P.F.M. / Djinovic-Carugo, K. / Baldwin, A.J. / Watkins, H. / Gehmlich, K. / Benesch, J.L.P.
History
DepositionMay 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein beta-1
B: Heat shock protein beta-1
E: Heat shock protein beta-1
F: Heat shock protein beta-1
G: Heat shock protein beta-1
H: Heat shock protein beta-1
C: Heat shock protein beta-1
D: Heat shock protein beta-1
K: ALA-LEU-SER-ARG-GLN
J: LEU-SER-GLY-VAL
L: ALA-LEU-SER-ARG
I: ALA-LEU-SER-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,67713
Polymers79,58412
Non-polymers921
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Native mass spectrometry supports dimeric assembly for this construct, rather than tetrameric or octameric as may be inferred from the structure.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9740 Å2
ΔGint-17 kcal/mol
Surface area43210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.810, 157.670, 57.870
Angle α, β, γ (deg.)90.000, 95.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABEFGHCD

#1: Protein
Heat shock protein beta-1 / Heat shock response / HspB1 / 28 kDa heat shock protein / Estrogen-regulated 24 kDa protein / Heat shock 27 kDa protein / ...HspB1 / 28 kDa heat shock protein / Estrogen-regulated 24 kDa protein / Heat shock 27 kDa protein / HSP 27 / Stress-responsive protein 27 / SRP27


Mass: 9717.790 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPB1, HSP27, HSP28 / Production host: Escherichia coli (E. coli) / References: UniProt: P04792

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Protein/peptide , 3 types, 4 molecules KJLI

#2: Protein/peptide ALA-LEU-SER-ARG-GLN


Mass: 574.651 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein/peptide LEU-SER-GLY-VAL


Mass: 374.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Protein/peptide ALA-LEU-SER-ARG


Mass: 446.522 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 372 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 3.24 Å3/Da / Density % sol: 62.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PEG 3350; 0.02 M sodium potassium diphosphate; 0.1 M Bis-Tris propane pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.1→78.84 Å / Num. obs: 57271 / % possible obs: 97.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 32.31 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.081 / Rrim(I) all: 0.144 / Net I/σ(I): 5.1 / Num. measured all: 165497 / Scaling rejects: 104
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.162.90.811283143560.5280.560.991.495.8
9.15-78.843.30.05325157530.9940.0330.06313.399.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.33 Å78.83 Å
Translation5.33 Å78.83 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
MOSFLMdata reduction
Aimless0.5.15data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MJH

4mjh


Resolution: 2.1→57.608 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.7
RfactorNum. reflection% reflection
Rfree0.2514 2773 4.85 %
Rwork0.2108 --
obs0.2127 57142 97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.38 Å2 / Biso mean: 42.2891 Å2 / Biso min: 14.99 Å2
Refinement stepCycle: final / Resolution: 2.1→57.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5534 0 6 371 5911
Biso mean--72.12 38.31 -
Num. residues----712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025775
X-RAY DIFFRACTIONf_angle_d0.5247870
X-RAY DIFFRACTIONf_chiral_restr0.048882
X-RAY DIFFRACTIONf_plane_restr0.0031041
X-RAY DIFFRACTIONf_dihedral_angle_d17.5343531
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.13630.35871390.31512674281396
2.1363-2.17510.30081480.31182613276194
2.1751-2.21690.32421300.30682651278195
2.2169-2.26220.36111470.29762622276994
2.2622-2.31140.30871440.29762645278995
2.3114-2.36520.30511320.29652621275394
2.3652-2.42430.29711430.28782661280495
2.4243-2.48990.28451430.272613275694
2.4899-2.56310.361290.26962673280296
2.5631-2.64580.28761320.26542725285797
2.6458-2.74040.31671420.26822737287998
2.7404-2.85010.32461420.2592776291899
2.8501-2.97980.28811640.23552748291299
2.9798-3.13690.27371270.2272743287098
3.1369-3.33350.28521350.213728012936100
3.3335-3.59080.24111330.18862790292399
3.5908-3.95210.20221250.174728092934100
3.9521-4.52380.15761350.14552825296099
4.5238-5.69870.15571200.13682830295099
5.6987-57.63010.24271630.17972812297599
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)
14.5216-3.78154.98223.1401-4.08645.3720.41190.6824-0.3862-0.4597-0.09550.64560.3720.2673-0.34460.4190.0454-0.12310.42830.04270.31793.0322-6.622434.039
27.6308-4.33-1.74672.43060.88493.47350.0104-0.3552-0.40730.0824-0.05990.10010.11950.06570.03980.380.0006-0.05520.20060.06830.2493-24.21888.339827.384
36.4529-3.82371.66086.59741.73412.6667-0.5405-1.10250.29780.76120.6299-0.7024-0.2274-0.0886-0.0830.52460.0604-0.02810.3705-0.03080.2737-37.344225.812830.629
47.5966-4.290.91944.2454-0.28913.6385-0.195-0.2641-0.26450.40930.1122-0.08350.14350.24210.06430.32710.0031-0.00010.23010.07540.2231-20.075.624626.305
56.5595-6.2887-4.88686.65695.27234.6890.124-0.53621.0182-0.1720.1597-1.4065-0.5270.5582-0.26130.3887-0.0852-0.10050.38280.01550.3813-35.96134.794417.8172
64.337-3.5184-0.15935.6550.51221.6698-0.10150.23190.12740.2895-0.15440.0733-0.1563-0.06480.22540.2908-0.0443-0.08140.20370.02770.1773-39.427925.374716.7651
74.2094-4.94385.56686.1523-6.35387.6347-0.27170.32870.220.4102-0.2801-0.1749-0.13360.20220.61980.22180.0469-0.00540.34870.0410.2775-57.38615.3206-33.4909
85.50933.807-5.36376.7144-5.18759.20450.08160.08770.2137-0.19240.26580.20850.1706-0.8725-0.44080.30720.0978-0.10850.42670.00230.2291-54.1642-9.9187-6.9661
92.88181.5821-0.6796.0794-4.24536.1830.1123-0.15360.20660.01640.20350.6118-0.4157-0.6131-0.24910.30510.117-0.04060.4822-0.03080.2545-53.181-11.5346-2.9504
106.11132.5306-2.08425.5743-4.32983.3417-0.57140.31820.4072-0.86570.39130.2675-0.6082-0.7683-0.08550.50540.0656-0.05470.42410.06730.2409-51.8217-4.5761-15.769
114.17973.1435-0.97556.3456-3.40493.45060.01940.3448-0.4428-0.74930.24740.08150.8726-0.2485-0.22690.49110.008-0.12970.3171-0.03710.3046-47.3471-32.90499.1589
122.54361.6564-2.27925.9363-4.1046.33430.2088-0.114-0.04760.0598-0.05480.25970.2825-0.1981-0.1420.2958-0.0398-0.10410.3425-0.05380.1752-46.5007-26.92269.2418
138.1429-5.2-7.6333.44234.9937.3073-0.52790.0039-0.50410.4484-0.15320.4302-0.0019-0.19170.71860.30310.04320.01750.2994-0.12510.2774-22.2648-47.4292-1.5326
147.57134.7955.45824.93946.46718.94140.09070.6408-0.196-1.010.2995-0.4448-0.54590.5168-0.25780.48740.0875-0.01690.3522-0.02180.2356-30.427-31.126215.7683
155.03932.54022.39336.81724.82433.55860.4495-0.0699-0.0070.010.2559-0.56130.28820.5435-0.72070.36920.05920.01620.3748-0.1180.3787-26.3372-29.742929.1799
164.82633.91473.7485.83865.63245.22910.2119-0.14170.00170.1371-0.1553-0.33250.34130.006-0.1030.40970.04590.00310.3275-0.03750.2728-30.3137-24.60532.9015
175.531.64631.38158.41584.86726.43260.17590.1711-0.1241-0.120.1598-0.28120.36690.4312-0.39570.33970.0746-0.02280.3098-0.03450.155-28.2893-36.555217.6612
189.26881.37610.9826.63661.37184.1578-0.31751.0391-0.381-0.41590.6913-0.1618-0.458-0.2198-0.49580.6824-0.03260.23550.62080.01990.6331-32.0031-1.474735.1741
193.3813.05291.2745.32363.50233.8664-0.53940.28320.6739-1.43430.17341.0343-1.3747-0.36150.4020.6268-0.0029-0.0260.28770.11660.45-35.68510.292339.355
203.00671.72030.80226.36225.08045.74710.0815-0.1376-0.09530.1057-0.1354-0.00130.1884-0.13420.04780.29630.0634-0.01880.23310.00070.1609-40.3723-19.130236.3992
212.4240.72221.9316.56652.85544.43590.0299-0.10240.1456-0.1098-0.1043-0.088-0.3047-0.11470.0910.2461-0.00330.04110.2280.02130.1172-37.5239-6.795542.3819
226.25471.8974-5.10780.5999-1.60594.20870.6212-0.23020.27130.7445-0.39970.3757-0.2173-0.0131-0.22330.3905-0.17680.09590.40470.02660.1906-25.560244.4462-7.0966
239.0056.69533.35186.45252.23521.4704-0.14930.1363-1.0292-0.44830.1294-0.9578-0.12240.1830.04680.4175-0.04510.0460.33880.08630.3395-47.89323.661-1.8319
248.27577.90746.92347.72595.38799.2021-0.4537-0.18780.7883-0.7646-0.30620.7693-0.602-0.81630.76550.38860.0081-0.0650.340.04720.2232-57.00629.7844-2.4564
258.41117.15453.03399.0484.21486.5737-0.44410.2770.0538-1.0676-0.15810.32330.1185-0.29680.3570.3982-0.02290.02330.38060.02730.2008-61.370416.7833-1.4288
263.81884.3712-0.16415.90370.6146.9171-0.23680.53030.15960.05730.3587-0.0095-0.44010.4213-0.1680.2959-0.0227-0.03150.37440.01250.2764-44.960232.7322-2.9188
275.22445.4467-4.31016.1665-3.24327.5407-0.058-1.180.1339-0.0515-0.20380.42560.09770.67290.22350.89370.14020.13480.7345-0.1460.9271-64.4394-4.98085.3167
287.61124.9622.29888.27044.32515.8369-0.03170.4118-0.14030.2917-0.18740.14580.37840.26970.18910.28340.0250.01970.3249-0.0090.1461-68.59999.0038.1151
296.34236.71333.19388.40615.08944.6533-0.1077-0.05530.05450.0088-0.14130.2199-0.2242-0.26040.28050.2791-0.0326-0.05930.36150.03210.2923-60.726818.81787.0311
306.15592.83370.92248.69093.75238.2423-0.0362-0.1259-0.407-0.25290.04440.24881.04920.0783-0.06520.42930.0067-0.01440.21870.03330.2479-71.63940.048310.0738
312.1278-1.1139-1.12647.73086.02664.73440.17430.31430.0425-2.07981.1603-1.68860.5296-0.6244-1.08731.014-0.04970.08360.9551-0.19860.7216-36.0711-25.48540.3584
325.10951.6414-1.11023.10071.76812.1313-0.9222-0.1265-0.6731-1.46160.8007-1.2933-0.72940.7754-0.18240.60050.12530.18841.3270.0420.5915-57.97539.47813.6891
336.41155.31842.87977.88162.11781.3111-0.5581-0.1788-0.63521.1876-0.26610.61790.985-0.86440.48410.9635-0.04760.22721.34590.07980.4193-47.5373-16.477329.1945
347.9908-7.0919-3.77567.81385.51034.8502-1.35443.278-1.4272-0.1556-0.277-0.34350.73431.66491.33410.76380.09450.29411.15160.28351.3022-29.186522.19668.2097
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 84 through 93 )A84 - 93
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 124 )A94 - 124
3X-RAY DIFFRACTION3chain 'A' and (resid 125 through 135 )A125 - 135
4X-RAY DIFFRACTION4chain 'A' and (resid 136 through 170 )A136 - 170
5X-RAY DIFFRACTION5chain 'B' and (resid 84 through 105 )B84 - 105
6X-RAY DIFFRACTION6chain 'B' and (resid 106 through 170 )B106 - 170
7X-RAY DIFFRACTION7chain 'E' and (resid 84 through 93 )E84 - 93
8X-RAY DIFFRACTION8chain 'E' and (resid 94 through 114 )E94 - 114
9X-RAY DIFFRACTION9chain 'E' and (resid 115 through 161 )E115 - 161
10X-RAY DIFFRACTION10chain 'E' and (resid 162 through 170 )E162 - 170
11X-RAY DIFFRACTION11chain 'F' and (resid 84 through 114 )F84 - 114
12X-RAY DIFFRACTION12chain 'F' and (resid 115 through 170 )F115 - 170
13X-RAY DIFFRACTION13chain 'G' and (resid 84 through 93 )G84 - 93
14X-RAY DIFFRACTION14chain 'G' and (resid 94 through 100 )G94 - 100
15X-RAY DIFFRACTION15chain 'G' and (resid 101 through 114 )G101 - 114
16X-RAY DIFFRACTION16chain 'G' and (resid 115 through 143 )G115 - 143
17X-RAY DIFFRACTION17chain 'G' and (resid 144 through 170 )G144 - 170
18X-RAY DIFFRACTION18chain 'H' and (resid 84 through 90 )H84 - 90
19X-RAY DIFFRACTION19chain 'H' and (resid 91 through 100 )H91 - 100
20X-RAY DIFFRACTION20chain 'H' and (resid 101 through 135 )H101 - 135
21X-RAY DIFFRACTION21chain 'H' and (resid 136 through 170 )H136 - 170
22X-RAY DIFFRACTION22chain 'C' and (resid 84 through 93 )C84 - 93
23X-RAY DIFFRACTION23chain 'C' and (resid 94 through 105 )C94 - 105
24X-RAY DIFFRACTION24chain 'C' and (resid 106 through 124 )C106 - 124
25X-RAY DIFFRACTION25chain 'C' and (resid 125 through 143 )C125 - 143
26X-RAY DIFFRACTION26chain 'C' and (resid 144 through 170 )C144 - 170
27X-RAY DIFFRACTION27chain 'D' and (resid 85 through 93 )D85 - 93
28X-RAY DIFFRACTION28chain 'D' and (resid 94 through 124 )D94 - 124
29X-RAY DIFFRACTION29chain 'D' and (resid 125 through 143 )D125 - 143
30X-RAY DIFFRACTION30chain 'D' and (resid 144 through 170 )D144 - 170
31X-RAY DIFFRACTION31chain 'K' and (resid 76 through 80 )K76 - 80
32X-RAY DIFFRACTION32chain 'J' and (resid 77 through 85 )J77 - 85
33X-RAY DIFFRACTION33chain 'L' and (resid 76 through 79 )L76 - 79
34X-RAY DIFFRACTION34chain 'I' and (resid 76 through 79 )I76 - 79

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