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- PDB-9h1f: Cofilin-1 in complex with high-affinity Sybody B12 -

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Basic information

Entry
Database: PDB / ID: 9h1f
TitleCofilin-1 in complex with high-affinity Sybody B12
Components
  • Cofilin-1
  • SybodyB12
KeywordsPROTEIN BINDING / Cofilin-1 / CFL1 / ADF/cofilin / G-Actin / F-Actin / Actin / Sybody / Nanobody / Synthetic Nanobody / Actin binding protein / ABP
Function / homology
Function and homology information


actin filament fragmentation / positive regulation of embryonic development / actin filament severing / establishment of spindle localization / regulation of dendritic spine morphogenesis / actin filament depolymerization / positive regulation by host of viral process / RHO GTPases Activate ROCKs / regulation of cell morphogenesis / mitotic cytokinesis ...actin filament fragmentation / positive regulation of embryonic development / actin filament severing / establishment of spindle localization / regulation of dendritic spine morphogenesis / actin filament depolymerization / positive regulation by host of viral process / RHO GTPases Activate ROCKs / regulation of cell morphogenesis / mitotic cytokinesis / lamellipodium membrane / Sema3A PAK dependent Axon repulsion / Rho protein signal transduction / cytoskeleton organization / EPHB-mediated forward signaling / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / response to virus / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / nuclear matrix / actin filament binding / Platelet degranulation / lamellipodium / actin cytoskeleton / actin cytoskeleton organization / growth cone / vesicle / focal adhesion / negative regulation of apoptotic process / extracellular space / extracellular exosome / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
ADF/Cofilin / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsParaschiakos, T. / Windhorst, S. / Pogenberg, V.
Funding support Germany, 2items
OrganizationGrant numberCountry
Other governmentHAMBURG INNOVATION C4T963 Germany
Other privateErich und Gertrud Roggenbuck-Stiftung Germany
CitationJournal: Biochem Pharmacol / Year: 2025
Title: A high affinity Sybody blocks Cofilin-1 binding to F-actin in vitro and in cancer cells.
Authors: Paraschiakos, T. / Li, J. / Scholz, J. / Han, S.J. / Deckers, M. / Pogenberg, V. / Faix, J. / Windhorst, S.
History
DepositionOct 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cofilin-1
B: SybodyB12


Theoretical massNumber of molelcules
Total (without water)31,7872
Polymers31,7872
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-7 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.575, 121.575, 52.346
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein Cofilin-1 / 18 kDa phosphoprotein / p18 / Cofilin / non-muscle isoform


Mass: 19135.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFL1, CFL / Production host: Escherichia coli (E. coli) / References: UniProt: P23528
#2: Protein SybodyB12


Mass: 12652.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.04 Å3/Da / Density % sol: 59.57 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Citric acid pH 4.0 and 2.4 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97623 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.8→29.49 Å / Num. obs: 36823 / % possible obs: 99.6 % / Redundancy: 26.6 % / Biso Wilson estimate: 38.24 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.085 / Net I/σ(I): 21.79
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 1.897 / Mean I/σ(I) obs: 1.36 / Num. unique obs: 3644 / CC1/2: 0.69

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MxCuBEdata collection
autoPROC1.1.7 (20210504)data processing
XDSVERSION Jun 30, 2023data reduction
Aimless0.7.15data scaling
PHASER2.8.3phasing
Coot0.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.49 Å / SU ML: 0.2837 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2035
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2263 1789 4.86 %
Rwork0.2026 35028 -
obs0.2037 36817 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 0 183 2278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01032138
X-RAY DIFFRACTIONf_angle_d1.01012887
X-RAY DIFFRACTIONf_chiral_restr0.0654323
X-RAY DIFFRACTIONf_plane_restr0.0076369
X-RAY DIFFRACTIONf_dihedral_angle_d12.6488796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.60091110.47392679X-RAY DIFFRACTION99.89
1.85-1.90.40191630.33622617X-RAY DIFFRACTION100
1.9-1.960.27561480.25792650X-RAY DIFFRACTION99.96
1.96-2.030.22861340.22012672X-RAY DIFFRACTION99.96
2.03-2.120.26291350.22332666X-RAY DIFFRACTION100
2.12-2.210.2721390.22372663X-RAY DIFFRACTION100
2.21-2.330.28731230.22882697X-RAY DIFFRACTION100
2.33-2.470.24041380.2142678X-RAY DIFFRACTION100
2.48-2.670.20131270.21312691X-RAY DIFFRACTION100
2.67-2.930.25361430.20482718X-RAY DIFFRACTION100
2.93-3.360.20241380.20212724X-RAY DIFFRACTION100
3.36-4.230.19591360.16392659X-RAY DIFFRACTION96.05
4.23-29.490.21241540.19432914X-RAY DIFFRACTION99.9
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)
16.41241288553-2.43940201379-5.672666442781.449493468672.082525061517.93468128616-0.1137729352290.184922376857-0.1061165420190.00821037541764-0.0392418510933-0.02384726185650.0802963086402-0.2036122542370.1058346609160.25371236309-0.006671040125430.01109765076220.190249961905-0.01558623721650.43332802859420.786177575214.87726959462.43661747815
20.378954597694-0.4935576950280.6188572616288.15306469051.392258092863.9082031861-0.107069200428-0.265431740733-0.09539812023760.5781739627380.249365036482-0.3050832639480.191444906696-0.162054499339-0.1518210744330.253851795631-0.0184958950122-0.005044698674140.2224618517460.0076314238840.31862931187420.867565209214.228059635514.5368857104
31.61783329887-0.467743780007-0.1995701141795.229799873551.190329186260.336156998950.320849957149-0.119560376289-0.1489603565880.7255611815640.188598119217-1.948640791220.1670829983320.251218963481-0.5786650462740.3584805326140.0378844620955-0.1034507821460.274126098269-0.03465606977710.6786024873132.19623752443.2728834529.55510601823
47.28101411711-2.42712740868-3.962978731849.52028188213.317829743579.353091199560.0711196860563-0.2269156183220.2864281295150.7424104972550.005039833366370.279767772934-0.423423790257-0.249351226507-0.1785163340410.320248421456-0.0107275356868-0.006691518887980.270501508063-0.03836420694830.40145194755722.642407507420.853699493319.2151299651
54.57146258065-4.422858937791.863750274634.31520898511-1.46608735178.94400385532-0.88047096508-1.32900707984-0.1882179948551.08340753210.6709882497-0.3334216834710.610965186221-0.5725567744950.009333341902110.4468417274830.08573780601310.07993941700080.5200679445870.04447650114770.54304315838720.1044519855-17.465679026120.9754590736
67.17915686109-5.746327820770.3412825708824.67249046187-0.7494652729192.42640960602-0.231690548449-0.284487772259-0.8972605830490.6125353655590.6362170821881.30658483690.997316525253-0.300066459884-0.3839833433330.3711874377740.04754893832370.0656968284660.4518521081990.09272754979410.50507213590427.6343414393-33.459542415619.1356344452
72.65665957052-1.85859784662-2.015522831065.040353283792.42387162128.292674560740.04762887332660.189536356507-0.4926687767790.237155869882-0.116308957720.9777830064070.177657706056-0.9037014758840.01020094703150.2836902665530.01184630983390.0442802259430.2738550973770.04548655564070.58768037109316.2343570928-16.252855855911.6732783066
85.36507584224-1.446271873231.445850036383.39587945665-2.044121305815.70708074770.05374441152180.0592245492594-0.470338734193-0.575601430897-0.0436898348992-0.07567613692630.6539027708210.283731450099-0.02037915881060.263705835249-0.0116509094603-0.001561183559410.209108909839-0.03215624251820.42837280205326.501498281-23.00535697723.94084722843
96.9264616612-4.267228571251.435567871927.00229879822-0.7951289958454.13924956026-0.181948360404-0.610003803665-0.3259103945170.2036120060650.306197304033-0.303974275970.08666800371220.348607270548-0.1203044969440.2186256028840.009030386196650.01677571396490.188237544107-0.0279413972910.33859254884731.8177561746-17.57352954611.5214004273
104.26579045155-2.942405914930.533658493444.01234881691-0.299952359152.81014865862-0.276693702082-0.250854248358-0.01262756492440.2563589754970.229002885591-0.269741468229-0.08301595362170.292697043458-0.01099954936170.207895417914-0.0222590322899-0.03392235310720.17275394855-0.01782575874050.44299325949632.1815069039-13.1518516929.60629187371
113.80692134378-1.161174035172.184480959368.45690153416-6.605900576618.77657762719-0.135310672189-0.3154887625650.2065813824950.94145103855-0.0248205594350.356518463591-0.366061168096-0.1995048507580.1723093738850.4111587626770.004104303980710.1051629546220.169139478344-0.03295754444880.48847386683719.4296910539-4.2846878099712.9356070065
128.06338603454-2.552497334462.843504350184.56084178858-1.399396184965.11420697878-0.1167701933890.1480860864610.5472764448880.1312301017550.0940455803529-1.03866748712-0.0240785153510.1259084189160.01464933695150.325889861803-0.003713448967920.04511155004260.244464359575-0.03833315986880.66673929253135.0039869852-10.83029127927.92421362058
136.302935282644.21246026553-1.787351467768.36242355084.17583488968.28311208870.1193029308480.2119286803241.25109428456-1.002373280780.0142143599898-0.37379639757-0.61126143245-0.346871584812-0.07820523239340.3077621704910.01342487786430.07134907146930.273739356340.009901022718910.73030089900243.6101591747-20.39621246875.73877143619
143.10347284015-2.90786288935-0.02396007624343.180919978691.346616162463.295944441590.1242899137250.05348039581340.3954822962790.1068076694690.07081746796-2.061849683790.4436547127540.794419526078-0.2812993881420.3165720333380.03441679542570.04919460891970.296408627079-0.01762329109630.70281385343835.065589846610.59511819385.35056529539
155.650033083672.708856226250.895226203333.06067761048-2.387605549574.651139089420.0724612781027-0.3412868081680.01841984344210.362630168798-0.1617051477920.353284914367-0.770283212056-0.608845925010.04661273689520.3763076926310.01722906557320.03232731419520.237771113928-0.09386598190510.44909092956319.837093966625.175387948615.8001771271
166.62395031955-1.57009377599-4.338066067561.104287952492.215433090277.822610528330.09832868329650.05901005776130.136486656111-0.3822079226620.105044403763-0.9151941031240.162050907930.321986752882-0.2125477266160.2826179755310.0253401063132.47093339213E-50.1800822381240.003386083887490.4739989014728.163044506610.17759114870.699995460269
177.790533808120.4653274210620.5349816774868.881756977374.837373694212.74990362520.013453123528-1.18101320322-0.254452253241.27013104471-0.252376602533-0.1358920631841.074443830890.06022917073980.2696334236520.419671033013-0.000873797504484-0.02510378460390.2933897498670.04135654082890.4371357312523.38437606387.5226740059416.3530544191
183.525530536460.3374256679911.460177531874.15952429902-0.3518983551059.79233596430.1175542053090.161592516777-0.20347072793-0.126413812741-0.05181174872680.3350003523830.529244113061-0.224393564402-0.02223238501910.257861073531-0.01539451404250.01775095595250.1794231349370.002651506456110.46220361816116.41830516826.424790858665.00307133542
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 67 through 85 )BB67 - 8565 - 83
22chain 'B' and (resid 86 through 100 )BB86 - 10084 - 98
33chain 'B' and (resid 101 through 109 )BB101 - 10999 - 107
44chain 'B' and (resid 110 through 116 )BB110 - 116108 - 114
55chain 'A' and (resid 12 through 25 )AA12 - 251 - 14
66chain 'A' and (resid 26 through 39 )AA26 - 3915 - 23
77chain 'A' and (resid 40 through 60 )AA40 - 6024 - 44
88chain 'A' and (resid 61 through 87 )AA61 - 8745 - 71
99chain 'A' and (resid 88 through 97 )AA88 - 9772 - 81
1010chain 'A' and (resid 98 through 117 )AA98 - 11782 - 101
1111chain 'A' and (resid 118 through 134 )AA118 - 134102 - 118
1212chain 'A' and (resid 135 through 164 )AA135 - 164119 - 148
1313chain 'A' and (resid 165 through 173 )AA165 - 173149 - 157
1414chain 'B' and (resid 3 through 9 )BB3 - 91 - 7
1515chain 'B' and (resid 10 through 19 )BB10 - 198 - 17
1616chain 'B' and (resid 20 through 35 )BB20 - 3518 - 33
1717chain 'B' and (resid 36 through 47 )BB36 - 4734 - 45
1818chain 'B' and (resid 48 through 66 )BB48 - 6646 - 64

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