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- PDB-5zz9: Crystal structure of Homer2 EVH1/Drebrin PPXXF complex -

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Basic information

Entry
Database: PDB / ID: 5zz9
TitleCrystal structure of Homer2 EVH1/Drebrin PPXXF complex
Components
  • Homer protein homolog 2
  • Peptide from Drebrin
KeywordsPROTEIN BINDING / POLYPROLINE RECOGNITION / SIGNALING PROTEIN
Function / homology
Function and homology information


positive regulation of receptor localization to synapse / G protein-coupled glutamate receptor binding / Neurexins and neuroligins / cell communication by chemical coupling / synaptic receptor adaptor activity / cell communication by electrical coupling / site of polarized growth / regulation of store-operated calcium entry / regulation of dendrite development / cytoplasmic sequestering of protein ...positive regulation of receptor localization to synapse / G protein-coupled glutamate receptor binding / Neurexins and neuroligins / cell communication by chemical coupling / synaptic receptor adaptor activity / cell communication by electrical coupling / site of polarized growth / regulation of store-operated calcium entry / regulation of dendrite development / cytoplasmic sequestering of protein / stereocilium tip / intracellular organelle / postsynaptic actin cytoskeleton organization / maintenance of protein location in cell / profilin binding / positive regulation of dendritic spine morphogenesis / positive regulation of synaptic plasticity / regulation of actin filament polymerization / actomyosin / gap junction / G protein-coupled glutamate receptor signaling pathway / regulation of G protein-coupled receptor signaling pathway / neural precursor cell proliferation / RHOD GTPase cycle / RHOBTB1 GTPase cycle / postsynaptic cytosol / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / cortical actin cytoskeleton / cortical cytoskeleton / regulation of neuronal synaptic plasticity / behavioral response to cocaine / RHOH GTPase cycle / : / glutamate receptor binding / positive regulation of axon extension / RHOBTB2 GTPase cycle / neuron projection morphogenesis / actin filament organization / sensory perception of sound / actin filament binding / actin cytoskeleton / lamellipodium / apical part of cell / actin binding / growth cone / postsynaptic membrane / in utero embryonic development / postsynaptic density / cytoskeleton / cadherin binding / protein domain specific binding / neuronal cell body / glutamatergic synapse / dendrite / protein-containing complex binding / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Homer, EVH1 domain / Homer family / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains ...Homer, EVH1 domain / Homer family / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Drebrin / Homer protein homolog 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi, Z. / Liu, H. / Li, J. / Liu, W. / Zhang, M.
Funding support China, 1items
OrganizationGrant numberCountry
Minister of Science and Technology of China2014CB910204 China
CitationJournal: Structure / Year: 2019
Title: Homer Tetramer Promotes Actin Bundling Activity of Drebrin.
Authors: Li, Z. / Liu, H. / Li, J. / Yang, Q. / Feng, Z. / Li, Y. / Yang, H. / Yu, C. / Wan, J. / Liu, W. / Zhang, M.
History
DepositionMay 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homer protein homolog 2
B: Homer protein homolog 2
C: Homer protein homolog 2
D: Peptide from Drebrin
E: Peptide from Drebrin
F: Peptide from Drebrin


Theoretical massNumber of molelcules
Total (without water)49,9186
Polymers49,9186
Non-polymers00
Water55831
1
A: Homer protein homolog 2
E: Peptide from Drebrin


Theoretical massNumber of molelcules
Total (without water)16,6392
Polymers16,6392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-12 kcal/mol
Surface area7590 Å2
MethodPISA
2
B: Homer protein homolog 2
D: Peptide from Drebrin


Theoretical massNumber of molelcules
Total (without water)16,6392
Polymers16,6392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-8 kcal/mol
Surface area6980 Å2
MethodPISA
3
C: Homer protein homolog 2
F: Peptide from Drebrin


Theoretical massNumber of molelcules
Total (without water)16,6392
Polymers16,6392
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-7 kcal/mol
Surface area6770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.337, 47.808, 50.415
Angle α, β, γ (deg.)70.440, 83.560, 90.390
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 9 through 47 or (resid 48...
21(chain B and (resid 9 through 59 or (resid 60...
31(chain C and (resid 9 or (resid 10 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUTHRTHR(chain A and (resid 9 through 47 or (resid 48...AA9 - 4711 - 49
12ARGARGARGARG(chain A and (resid 9 through 47 or (resid 48...AA4850
13GLYGLYASPASP(chain A and (resid 9 through 47 or (resid 48...AA8 - 12110 - 123
14GLYGLYASPASP(chain A and (resid 9 through 47 or (resid 48...AA8 - 12110 - 123
15GLYGLYASPASP(chain A and (resid 9 through 47 or (resid 48...AA8 - 12110 - 123
16GLYGLYASPASP(chain A and (resid 9 through 47 or (resid 48...AA8 - 12110 - 123
21GLUGLUALAALA(chain B and (resid 9 through 59 or (resid 60...BB9 - 5911 - 61
22LYSLYSLYSLYS(chain B and (resid 9 through 59 or (resid 60...BB6062
23GLYGLYASPASP(chain B and (resid 9 through 59 or (resid 60...BB8 - 12110 - 123
24GLYGLYASPASP(chain B and (resid 9 through 59 or (resid 60...BB8 - 12110 - 123
25GLYGLYASPASP(chain B and (resid 9 through 59 or (resid 60...BB8 - 12110 - 123
26GLYGLYASPASP(chain B and (resid 9 through 59 or (resid 60...BB8 - 12110 - 123
31GLUGLUGLUGLU(chain C and (resid 9 or (resid 10 and (name...CC911
32GLNGLNGLNGLN(chain C and (resid 9 or (resid 10 and (name...CC1012
33GLUGLUASPASP(chain C and (resid 9 or (resid 10 and (name...CC9 - 12111 - 123
34GLUGLUASPASP(chain C and (resid 9 or (resid 10 and (name...CC9 - 12111 - 123
35GLUGLUASPASP(chain C and (resid 9 or (resid 10 and (name...CC9 - 12111 - 123
36GLUGLUASPASP(chain C and (resid 9 or (resid 10 and (name...CC9 - 12111 - 123

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Components

#1: Protein Homer protein homolog 2 / Homer-2 / Cupidin / VASP/Ena-related gene up-regulated during seizure and LTP 2 / Vesl-2


Mass: 13549.175 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Homer2, Vesl2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QWW1
#2: Protein/peptide Peptide from Drebrin / Developmentally-regulated brain protein


Mass: 3090.282 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DBN1, D0S117E / Production host: Escherichia coli (E. coli) / References: UniProt: Q16643
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.05 Å3/Da / Density % sol: 39.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 50mM Ammonium fluoride, 8% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9776 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9776 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 17008 / % possible obs: 96.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.04 / Rrim(I) all: 0.076 / Χ2: 0.54 / Net I/σ(I): 5.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.343.60.4747970.8240.290.5570.46994.5
2.34-2.383.70.4318760.8530.2590.5040.4595
2.38-2.433.60.4198150.8650.2550.4920.47194.2
2.43-2.483.60.378320.8750.2260.4350.43296.3
2.48-2.533.60.2938830.9280.1810.3450.47496.6
2.53-2.593.50.2648270.9330.1620.3110.50297.1
2.59-2.663.50.2278890.9550.1410.2680.46596.2
2.66-2.733.30.1818210.9480.1190.2180.4996.8
2.73-2.813.40.1538600.9670.0970.1820.48996.6
2.81-2.93.30.1328290.9780.0860.1580.51496.6
2.9-33.70.1238940.9840.0740.1440.597.2
3-3.123.70.0978370.9890.0580.1130.56296.4
3.12-3.263.70.0828430.9910.0490.0960.59197.3
3.26-3.443.60.0718640.9930.0430.0830.65297
3.44-3.653.60.0578630.9940.0350.0680.64997
3.65-3.933.30.058440.9950.0330.060.62297.1
3.93-4.333.30.0458540.9960.0290.0530.68997.3
4.33-4.953.70.0418520.9980.0240.0470.64896.2
4.95-6.243.70.0398580.9980.0240.0460.54396.9
6.24-503.50.0358700.9970.0220.0410.58598.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX(1.12_2829: ???)refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DDV

1ddv


Resolution: 2.3→47.153 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.15 / Phase error: 25.54
RfactorNum. reflection% reflection
Rfree0.2281 821 4.83 %
Rwork0.1916 --
obs0.1934 16992 96.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 160.06 Å2 / Biso mean: 50.3153 Å2 / Biso min: 26.69 Å2
Refinement stepCycle: final / Resolution: 2.3→47.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 0 31 2963
Biso mean---45.45 -
Num. residues----387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043013
X-RAY DIFFRACTIONf_angle_d0.7824124
X-RAY DIFFRACTIONf_chiral_restr0.052477
X-RAY DIFFRACTIONf_plane_restr0.004538
X-RAY DIFFRACTIONf_dihedral_angle_d11.1491835
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1454X-RAY DIFFRACTION13.686TORSIONAL
12B1454X-RAY DIFFRACTION13.686TORSIONAL
13C1454X-RAY DIFFRACTION13.686TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.297-2.44090.29971130.26022623273693
2.4409-2.62940.2851360.24942713284997
2.6294-2.8940.28211470.23472677282497
2.894-3.31260.26461190.22772764288397
3.3126-4.17320.22031520.18022697284997
4.1732-47.16270.18491540.14812697285197
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)
14.6372-1.72970.72537.4229-4.23944.95030.17410.1499-0.7129-0.6804-0.08170.09630.87990.4791-0.03820.44510.0281-0.03430.2957-0.0810.36932.488127.3194-14.1092
22.0489-0.4540.99582.0516-1.20425.30570.0653-0.0323-0.01160.0370.0080.10770.11730.0157-0.03040.2768-0.00760.03330.1752-0.03260.2163-4.225434.5165-15.3795
36.33251.55511.88466.67823.03396.4324-0.0492-0.40430.12430.6617-0.04490.20550.1164-0.17760.09270.2624-0.0650.04220.23620.01280.2629-13.204657.4203-25.9491
43.21911.83980.57255.1701-0.12312.7562-0.01270.01060.11430.02770.03590.17840.0142-0.0493-0.00790.23320.01840.00590.2010.01670.176-19.259853.1947-32.4102
52.92221.3184-2.52642.7472-0.24962.68040.2011-0.273-0.19080.10040.2019-0.4257-0.12251.1391-0.51490.29750.0161-0.0390.55560.01360.412917.498530.8609-40.3003
68.66962.4439-5.00447.9659-1.21622.8936-0.5812.07430.7182-1.24450.84240.3928-0.55440.3736-0.29070.7746-0.08750.07140.81210.03060.47816.590534.2031-56.0332
77.53522.6208-5.17196.2063-0.04526.13770.33360.07340.68850.5120.267-0.1343-0.4740.2589-0.60380.3797-0.00820.05070.386-0.02130.260311.976535.1039-34.666
80.93420.3279-1.81325.95652.71035.3914-0.21510.19170.031-0.16290.08030.2849-0.0099-0.00450.1540.3038-0.0416-0.05810.36370.04550.296510.690329.8186-44.3216
98.62350.6813-4.28854.72110.06696.854-0.0573-0.0682-0.2673-0.05980.0008-0.05180.23580.19160.02030.2816-0.0151-0.01760.252-0.03190.23949.20526.3331-41.4769
100.4227-0.6726-0.6368.7683.85582.8259-1.6191.25110.84620.16190.0031.651-0.1237-1.89991.48590.5052-0.014-0.01140.83340.08550.7412-18.691869.1699-27.9444
119.50795.5332-2.96598.8882.06573.4609-0.15190.83820.10710.35450.65660.046-0.2664-0.9683-0.40580.4231-0.03120.02340.40210.05860.5101-8.172971.8259-33.7695
122.57823.6404-2.1048.27290.22775.8114-0.33040.4297-0.63810.52280.29740.38880.723-0.8796-0.08510.643-0.10490.04480.60330.03890.4642-7.020821.5313-3.7338
132.61190.7913-4.17342.2533-1.61296.7732-0.1794-1.3061-0.12241.3064-0.0630.17860.5272.50880.39060.76860.103-0.15230.8542-0.0390.50976.844727.05163.3537
146.112-6.0423-3.76948.32232.16736.33080.5921.32620.211-0.2454-0.9468-0.0198-1.0081-1.36410.41590.51060.17130.07170.64380.17140.52914.39924.6757-57.2638
158.67875.4214-5.07718.0209-7.7827.5584-0.4184-0.3017-0.6245-1.74080.458-0.89720.41781.0839-0.02130.5847-0.08370.12330.6569-0.23120.675421.502118.7688-55.4404
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 37 )A8 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 121 )A38 - 121
3X-RAY DIFFRACTION3chain 'B' and (resid 8 through 37 )B8 - 37
4X-RAY DIFFRACTION4chain 'B' and (resid 38 through 121 )B38 - 121
5X-RAY DIFFRACTION5chain 'C' and (resid 9 through 22 )C9 - 22
6X-RAY DIFFRACTION6chain 'C' and (resid 23 through 37 )C23 - 37
7X-RAY DIFFRACTION7chain 'C' and (resid 38 through 57 )C38 - 57
8X-RAY DIFFRACTION8chain 'C' and (resid 58 through 79 )C58 - 79
9X-RAY DIFFRACTION9chain 'C' and (resid 80 through 121 )C80 - 121
10X-RAY DIFFRACTION10chain 'D' and (resid 997 through 1003 )D997 - 1003
11X-RAY DIFFRACTION11chain 'D' and (resid 1004 through 1011 )D1004 - 1011
12X-RAY DIFFRACTION12chain 'E' and (resid 993 through 1003 )E993 - 1003
13X-RAY DIFFRACTION13chain 'E' and (resid 1004 through 1011 )E1004 - 1011
14X-RAY DIFFRACTION14chain 'F' and (resid 999 through 1003 )F999 - 1003
15X-RAY DIFFRACTION15chain 'F' and (resid 1004 through 1010 )F1004 - 1010

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