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- PDB-9hae: Dust mite allergen Der f 7 with computationally designed DerF7_b2... -

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Basic information

Entry
Database: PDB / ID: 9hae
TitleDust mite allergen Der f 7 with computationally designed DerF7_b2 binder
Components
  • DerF7_binder2
  • Mite allergen Der f 7
KeywordsDE NOVO PROTEIN / dust mite / allergen / der f 7 / computational / de novo / binder
Function / homologyMite allergen, group-7 / Mite allergen, group-7 superfamily / Group 7 allergen / extracellular region / Mite allergen Der f 7
Function and homology information
Biological speciesDermatophagoides farinae (American house dust mite)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsPacesa, M. / Nickel, L. / Correia, B.E.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: bioRxiv / Year: 2024
Title: BindCraft: one-shot design of functional protein binders.
Authors: Martin Pacesa / Lennart Nickel / Christian Schellhaas / Joseph Schmidt / Ekaterina Pyatova / Lucas Kissling / Patrick Barendse / Jagrity Choudhury / Srajan Kapoor / Ana Alcaraz-Serna / ...Authors: Martin Pacesa / Lennart Nickel / Christian Schellhaas / Joseph Schmidt / Ekaterina Pyatova / Lucas Kissling / Patrick Barendse / Jagrity Choudhury / Srajan Kapoor / Ana Alcaraz-Serna / Yehlin Cho / Kourosh H Ghamary / Laura Vinué / Brahm J Yachnin / Andrew M Wollacott / Stephen Buckley / Adrie H Westphal / Simon Lindhoud / Sandrine Georgeon / Casper A Goverde / Georgios N Hatzopoulos / Pierre Gönczy / Yannick D Muller / Gerald Schwank / Daan C Swarts / Alex J Vecchio / Bernard L Schneider / Sergey Ovchinnikov / Bruno E Correia
Abstract: Protein-protein interactions (PPIs) are at the core of all key biological processes. However, the complexity of the structural features that determine PPIs makes their design challenging. We present ...Protein-protein interactions (PPIs) are at the core of all key biological processes. However, the complexity of the structural features that determine PPIs makes their design challenging. We present BindCraft, an open-source and automated pipeline for protein binder design with experimental success rates of 10-100%. BindCraft leverages the weights of AlphaFold2 to generate binders with nanomolar affinity without the need for high-throughput screening or experimental optimization, even in the absence of known binding sites. We successfully designed binders against a diverse set of challenging targets, including cell-surface receptors, common allergens, designed proteins, and multi-domain nucleases, such as CRISPR-Cas9. We showcase the functional and therapeutic potential of designed binders by reducing IgE binding to birch allergen in patient-derived samples, modulating Cas9 gene editing activity, and reducing the cytotoxicity of a foodborne bacterial enterotoxin. Lastly, we utilize cell surface receptor-specific binders to redirect AAV capsids for targeted gene delivery. This work represents a significant advancement towards a "one design-one binder" approach in computational design, with immense potential in therapeutics, diagnostics, and biotechnology.
History
DepositionNov 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_CSD / _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: Mite allergen Der f 7
B: DerF7_binder2
C: Mite allergen Der f 7
D: DerF7_binder2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8067
Polymers69,7384
Non-polymers693
Water2,342130
1
A: Mite allergen Der f 7
B: DerF7_binder2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8923
Polymers34,8692
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Mite allergen Der f 7
D: DerF7_binder2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9154
Polymers34,8692
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.710, 90.250, 63.410
Angle α, β, γ (deg.)90.000, 93.024, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 6 through 23 or resid 25...
d_2ens_1(chain "C" and (resid 6 through 23 or resid 25...
d_1ens_2(chain "B" and (resid 6 through 20 or resid 22...
d_2ens_2(chain "D" and (resid 6 through 20 or resid 22...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ASPASPILEILEAA6 - 2314 - 31
d_12ens_1GLNGLNGLNGLNAA2533
d_13ens_1GLUGLUVALVALAA27 - 7535 - 83
d_14ens_1GLYGLYPHEPHEAA77 - 14085 - 148
d_15ens_1VALVALLYSLYSAA142 - 195150 - 203
d_21ens_1ASPASPILEILECC6 - 2314 - 31
d_22ens_1GLNGLNGLNGLNCC2533
d_23ens_1GLUGLUVALVALCC27 - 7535 - 83
d_24ens_1GLYGLYPROPROCC77 - 13085 - 138
d_25ens_1ILEILEPHEPHECC135 - 140143 - 148
d_26ens_1VALVALLYSLYSCC142 - 195150 - 203
d_11ens_2LYSLYSGLUGLUBB6 - 2014 - 28
d_12ens_2LEULEUPHEPHEBB22 - 2630 - 34
d_13ens_2GLUGLUVALVALBB28 - 3136 - 39
d_14ens_2GLUGLUILEILEBB33 - 4541 - 53
d_15ens_2VALVALGLUGLUBB57 - 7965 - 87
d_21ens_2LYSLYSGLUGLUDD6 - 2014 - 28
d_22ens_2LEULEUPHEPHEDD22 - 2630 - 34
d_23ens_2GLUGLUVALVALDD28 - 3136 - 39
d_24ens_2GLUGLUILEILEDD33 - 4541 - 53
d_25ens_2VALVALGLUGLUDD57 - 7965 - 87

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.9953691799, -0.0259649920116, -0.0925527681681), (0.0265625698252, -0.999633469211, -0.00523040325998), (-0.0923830373501, -0.00766462157041, 0.995694043362)45.4403017184, -13.8754465409, 31.0566141495
2given(-0.990648730515, -0.0574875998262, -0.123734670139), (0.0607035335093, -0.997904998201, -0.0223762281389), (-0.122189090134, -0.0296781136946, 0.992063020085)44.9482344715, -14.5055360408, 31.2875662452

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Components

#1: Protein Mite allergen Der f 7 / Allergen Der f VII


Mass: 22889.014 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dermatophagoides farinae (American house dust mite)
Gene: DERF7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q26456
#2: Protein DerF7_binder2


Mass: 11979.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.5, 0.2 M KSCN, 25 % w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.22→42.93 Å / Num. obs: 50681 / % possible obs: 95.22 % / Redundancy: 1.4 % / Biso Wilson estimate: 46.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0578 / Net I/σ(I): 6.25
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.6403 / Mean I/σ(I) obs: 0.94 / Num. unique obs: 5051 / CC1/2: 0.643 / % possible all: 96.34

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Processing

Software
NameVersionClassification
PHENIXdev_5316refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→42.93 Å / SU ML: 0.331 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6968
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2358 1461 4.92 %
Rwork0.2015 28230 -
obs0.2032 29691 95.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.51 Å2
Refinement stepCycle: LAST / Resolution: 2.22→42.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4220 0 3 130 4353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034291
X-RAY DIFFRACTIONf_angle_d0.69015761
X-RAY DIFFRACTIONf_chiral_restr0.0468644
X-RAY DIFFRACTIONf_plane_restr0.0057739
X-RAY DIFFRACTIONf_dihedral_angle_d11.0621669
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.60602453417
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.520181988898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.30.34191450.29432847X-RAY DIFFRACTION96.42
2.3-2.390.31441400.27692847X-RAY DIFFRACTION96.39
2.39-2.50.36791740.282818X-RAY DIFFRACTION96.83
2.5-2.630.29461540.24612876X-RAY DIFFRACTION97.15
2.63-2.790.26551780.23522856X-RAY DIFFRACTION96.84
2.79-3.010.27651430.23632835X-RAY DIFFRACTION96.66
3.01-3.310.27351270.21852802X-RAY DIFFRACTION93.67
3.31-3.790.29271140.19852597X-RAY DIFFRACTION86.72
3.79-4.770.19071320.16332897X-RAY DIFFRACTION97.05
4.77-42.930.16741540.17182855X-RAY DIFFRACTION94.56
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)
10.115095835150.00342216786573-0.11780769740.021617363084-0.05305197284750.2873207325150.380000360648-0.05895118006290.4649674239990.543580531475-0.1043139237950.09803892160540.0216977205712-0.6309584822920.01509775508120.517278340241-0.0448805990866-0.05875201826580.570221452497-0.008516332550190.363131634235-8.853689400063.7073150155229.4683290341
20.0297478059859-0.03593355324760.002006840456370.04297049477210.01162752384130.0255706887475-0.0903520187197-0.02270975480760.670297710133-0.032265942655-0.0274436009914-0.143095843991-0.00667272507632-0.388009174003-8.37802512674E-50.5901904243310.04815402054510.04577341163520.527845286233-0.03936917084440.508299996594-6.213203928362.674587636296.67656637709
30.106910369329-0.0970854730255-0.1571214327650.04283946425830.07711842058680.1144835137120.3630238462730.1020733788020.6379760990550.1396955701120.050595450215-0.318589048609-0.7012529753150.3670864050680.004090700479130.599733607352-0.04509345791020.1402351984970.5652450391140.06082659440.61178835191117.6766901105-2.72987165837-4.48724308285
40.2047942525820.0689925353248-0.09948024381830.158233241386-0.09252410306230.05382570086860.205100497245-0.176023951162-0.013481222271-0.0531664444839-0.150439569725-0.0406064969846-0.0823267312469-0.1279852027760.000173244945210.389734080204-0.0572693113576-0.006958671469360.410378261390.01957688721050.357432686111-1.426775669741.1351562987322.826272884
50.0554779111020.0009588497673564.58225822329E-50.0372665468129-0.05411002801320.07251441658170.0631153847683-0.50944908727-0.08954732490290.161477657698-0.108082317686-0.02193262975760.1287873858760.3257947909016.28645095794E-50.533637460969-0.0439147360255-0.06399033518940.559144670915-0.01230852704350.4480781516210.8610129899620.21796979563225.6731228758
60.4911052270070.135221354793-0.08285744628520.443105405096-0.1826703879660.2200621511480.1070960223340.06902718896360.123051257063-0.0805884805850.0694187978763-0.1305690682860.06212580465880.07736880727790.0002221542740220.4152269869020.01089486651010.02930327940960.476609370730.005305048474640.411036383255.08578793028-3.986825035094.65703539422
70.2066697573080.0997834233720.03295584968340.371728741793-0.2110470311480.3894216102040.296579981381-0.1149583128740.0737442879564-0.3715166777220.000202797429943-0.257526171358-0.367814370970.1458605431860.000198830210340.359701553875-0.01727946220090.02509805328440.340719858197-0.02789036821870.4258361697885.632394661330.33205352526410.8585602425
80.353386785197-0.08088200911520.1540876824860.4399844527120.1724527728810.406421992352-0.02909784360490.544250222792-0.177443047325-0.489694464451-0.0762720719999-0.8079274348390.4887059107080.4891253773440.004051434357140.5269032567690.1246783824960.08793476373520.5383277547010.01022436737780.65338981679621.9291455867-24.8113739953-5.25802648304
90.01559145835880.0110857427934-0.03781481697910.0106244809691-0.0008924985230270.0649609743958-0.07609301284470.2574972891510.08766631693840.127077985130.0593568320918-0.2149281471640.4459991635110.175806534655-0.0001984862694380.914761114871-0.1054855546260.01477380940981.28780268462-0.1390397667950.9079405143728.8054238925-21.10745238066.98028001855
100.0392730932157-0.03365752470.02656737866920.0319738596738-0.01025171301560.08258570817650.146702953297-0.3350260901110.01040066891340.1151165529380.05335397481010.135456085240.132487398172-0.265450495294-0.000375461134580.682771001989-0.0368796581957-0.03960017563420.6956213001990.1488458248830.5722691464515.3815084719-24.48660551085.9291627229
110.1173935209940.1382257278350.08100415831360.1276050095520.09796307488740.06461290912110.116294828343-0.0407382644545-0.3293461605740.26586044331-0.29274638430.1704932794370.3818160105920.04788957709590.0004320634164810.5415546642730.01528213870780.03587011152110.4002532772230.02768869591490.36307233235750.6986100135-18.016002916762.1969929126
120.0217182094332-0.003529326975010.01677995507140.02498504751750.01588571227750.000885272531832-0.109175979031-0.200898015092-0.1459236017030.09842182821460.0292032108271-0.1815550827750.3846232710350.5377963778010.0002153046962830.4225577495520.0739841035433-0.06127801666230.563302842804-0.0213118826370.42690017132950.4682243103-16.552371447238.0426723852
130.7601189666810.0677905162861.090106068370.6335591467670.6281404595712.141304251720.573917918861-0.1841064343520.2165673132020.2399294142360.1872179243480.5647924060620.435424422204-0.4383493471860.2129466115460.493223781753-0.215035193640.02615514081970.7999932328190.1060309954790.77123223561926.0664795071-10.5358004426.1196350916
140.5352845815920.15122802907-0.01491367013510.465467961996-0.3095064142320.2917939495620.08259379217990.0505572560520.2617150504790.056230179233-0.08903348142910.2043343585760.139782768532-0.04104080244620.001621579429650.470272690788-0.00846698598113-0.03481593557430.417498404916-0.03304535546110.40458951847940.3675089361-13.743404965244.2101267035
150.0940786971523-0.0388638403744-0.002150161145410.0195927574613-0.01951794088370.008380458891640.0921919224603-0.06954059898030.1971930713380.01551284763610.0455821059599-0.0662385764572-0.0676207431785-0.2578013533150.000372152427460.470964609457-0.0805667817299-0.02650335750210.4216014038220.05578781987920.48358665125542.1766465956-14.362545203656.4838564227
160.321014490066-0.04635944672720.1293619901040.4070411251730.02780126592380.332266442470.01474920194770.350112427381-0.1975383664870.1310871789680.4357776177220.101022886267-0.0359333050488-0.02804841609810.01975972590080.402108662555-0.0232879651934-0.05632003656670.5740088928960.07626312860770.42380669223439.6591559644-6.3641674895228.5560660229
170.2184354980740.0357227176969-0.1166243717750.106799657479-0.02518950872050.0647065298361-0.00928084358472-0.0449037593111-0.063178320498-0.257863894585-0.1473440603810.242538362850.6846783134460.1670451887477.3983876879E-50.5127319758560.0280718171153-0.002947009352340.4207120234750.04439543387210.42057017747942.9510638475-24.841286736557.5703979227
180.3694959253250.283862070918-0.3997600389060.204698356235-0.2487110940520.5169835884990.005372479108430.08689314630820.101795639388-0.04724786546660.2898706318440.1764213284960.184492229376-0.2744008175380.0001861866666060.4432300294590.0358908062823-0.03302761987980.4238814965350.0461041405680.44400370710938.2753129135-12.238435929239.0478748707
190.6129472225890.4167178863740.5188400913310.5159465373690.6121430995680.8041185633480.370521585810.389403921266-0.1238699003730.0208975028320.2268688658510.01717799422980.176613679777-0.1419225092760.6328468839950.6129829701190.0993733461497-0.03855287757781.058713860440.5757287352941.0243331240730.841060316712.214501079421.9634400373
200.111523058499-0.1235340408450.178893096520.3597654511530.1195576949710.5023262050850.4327940019530.21666329486-0.194229519766-0.1494036947310.2976955598770.4923997102780.16037850729-0.4433335882750.9407653843720.2078456105840.333886340955-0.222143262541.310951122691.097295074971.8772600851819.6055025117.1701009837521.8795811281
210.00305654741729-0.003149934494030.008857172544980.00821252866299-0.006932695122420.00842664344359-0.05495626639750.0716333599027-0.09650819940310.0604683979889-0.04499960277950.1365896240190.06952849400930.0763385555002-0.0001056911861191.030975201970.1441837890960.23774093441.420577353380.1850827376991.6022845524416.87290470536.7038103930535.2662082444
220.0152714387425-0.0003034237711940.02711381915090.0217180583307-0.01625334880340.0373362655424-0.00599212096811-0.2047639130940.08906487722050.6472144559890.305003739510.3308476385210.0123712539673-0.4927485778420.0006760299607080.8569715029870.3077991304650.2386822755630.8394708426750.1368713155221.2261850991229.42714538099.8544485166136.0145494943
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 25 )AA6 - 251 - 20
22chain 'A' and (resid 26 through 36 )AA26 - 3621 - 31
33chain 'A' and (resid 37 through 57 )AA37 - 5732 - 52
44chain 'A' and (resid 58 through 80 )AA58 - 8053 - 75
55chain 'A' and (resid 81 through 94 )AA81 - 9476 - 89
66chain 'A' and (resid 95 through 129 )AA95 - 12990 - 124
77chain 'A' and (resid 130 through 195 )AA130 - 195125 - 186
88chain 'B' and (resid 1 through 49 )BB1 - 491 - 49
99chain 'B' and (resid 50 through 63 )BB50 - 6350 - 58
1010chain 'B' and (resid 64 through 81 )BB64 - 8159 - 76
1111chain 'C' and (resid 5 through 25 )CC5 - 251 - 21
1212chain 'C' and (resid 26 through 36 )CC26 - 3622 - 32
1313chain 'C' and (resid 37 through 47 )CC37 - 4733 - 43
1414chain 'C' and (resid 48 through 80 )CC48 - 8044 - 76
1515chain 'C' and (resid 81 through 94 )CC81 - 9477 - 90
1616chain 'C' and (resid 95 through 120 )CC95 - 12091 - 116
1717chain 'C' and (resid 121 through 142 )CC121 - 142117 - 138
1818chain 'C' and (resid 143 through 195 )CC143 - 195139 - 191
1919chain 'D' and (resid 5 through 24 )DD5 - 241 - 20
2020chain 'D' and (resid 25 through 44 )DD25 - 4421 - 40
2121chain 'D' and (resid 45 through 63 )DD45 - 6341 - 49
2222chain 'D' and (resid 64 through 79 )DD64 - 7950 - 65

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