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- PDB-7rah: Adenylate cyclase toxin RTX domain fragment bound to M1H5 Fab and... -

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Basic information

Entry
Database: PDB / ID: 7rah
TitleAdenylate cyclase toxin RTX domain fragment bound to M1H5 Fab and M2B10 Fab
Components
  • Bifunctional adenylate cyclase toxin/hemolysin CyaA,Bifunctional adenylate cyclase toxin/hemolysin CyaA
  • M1H5 Fab Heavy Chain
  • M1H5 Fab Light Chain
  • M2B10 Fab Heavy Chain
  • M2B10 Fab Light Chain
KeywordsIMMUNE SYSTEM/TOXIN / RTX / Toxin / Complex / IMMUNE SYSTEM-TOXIN complex
Function / homology
Function and homology information


calcium- and calmodulin-responsive adenylate cyclase activity / channel activity / toxin activity / killing of cells of another organism / calcium ion binding / extracellular region / membrane
Similarity search - Function
RTX, pore-forming domain / N-terminal domain in RTX protein / Haemolysin-type calcium binding-related / Haemolysin-type calcium binding protein related domain / RTX toxin determinant A / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / Hemolysin-type calcium-binding conserved site ...RTX, pore-forming domain / N-terminal domain in RTX protein / Haemolysin-type calcium binding-related / Haemolysin-type calcium binding protein related domain / RTX toxin determinant A / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal
Similarity search - Domain/homology
PHOSPHATE ION / Cyclolysin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Bordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGoldsmith, J.A. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI122753 United States
CitationJournal: Plos Pathog. / Year: 2021
Title: Structural basis for antibody binding to adenylate cyclase toxin reveals RTX linkers as neutralization-sensitive epitopes.
Authors: Goldsmith, J.A. / DiVenere, A.M. / Maynard, J.A. / McLellan, J.S.
History
DepositionJul 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: M1H5 Fab Light Chain
B: M1H5 Fab Heavy Chain
C: M2B10 Fab Light Chain
D: M2B10 Fab Heavy Chain
E: Bifunctional adenylate cyclase toxin/hemolysin CyaA,Bifunctional adenylate cyclase toxin/hemolysin CyaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,49425
Polymers145,6375
Non-polymers85620
Water3,387188
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11000 Å2
ΔGint-138 kcal/mol
Surface area51350 Å2
Unit cell
Length a, b, c (Å)65.559, 117.020, 254.709
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules E

#5: Protein Bifunctional adenylate cyclase toxin/hemolysin CyaA,Bifunctional adenylate cyclase toxin/hemolysin CyaA / Cyclolysin


Mass: 48447.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: cya, cyaA, FF138_04025, NCTC10911_01123 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A380ZZA1

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Antibody , 4 types, 4 molecules ABCD

#1: Antibody M1H5 Fab Light Chain


Mass: 23812.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody M1H5 Fab Heavy Chain


Mass: 25098.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody M2B10 Fab Light Chain


Mass: 23207.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Antibody M2B10 Fab Heavy Chain


Mass: 25071.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 208 molecules

#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.35 Å3/Da / Density % sol: 63.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1M sodium potassium phosphate pH 6.2, 10% PEG8000, 0.2M NaCl, 3% sucrose

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→86.17 Å / Num. obs: 61228 / % possible obs: 100 % / Redundancy: 5.7 % / Biso Wilson estimate: 52.83 Å2 / CC1/2: 0.983 / Net I/σ(I): 7.4
Reflection shellResolution: 2.6→2.67 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4468 / CC1/2: 0.771 / % possible all: 100

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Processing

Software
NameVersionClassification
Coot1.19.1_4122+SVNmodel building
PHENIX1.19.1_4122+SVNrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5cvw

5cvw


Resolution: 2.6→55.81 Å / SU ML: 0.2987 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.4337
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2176 3070 5.03 %
Rwork0.195 58023 -
obs0.1962 61093 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.77 Å2
Refinement stepCycle: LAST / Resolution: 2.6→55.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8971 0 24 188 9183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00219163
X-RAY DIFFRACTIONf_angle_d0.547512442
X-RAY DIFFRACTIONf_chiral_restr0.04321374
X-RAY DIFFRACTIONf_plane_restr0.00391619
X-RAY DIFFRACTIONf_dihedral_angle_d5.0321269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.640.26731170.25622618X-RAY DIFFRACTION99.82
2.64-2.680.27621320.25912608X-RAY DIFFRACTION99.82
2.68-2.730.28031460.24422630X-RAY DIFFRACTION99.82
2.73-2.780.26641230.24582560X-RAY DIFFRACTION99.78
2.78-2.830.29541420.26292630X-RAY DIFFRACTION99.93
2.83-2.890.39261570.28792560X-RAY DIFFRACTION99.6
2.89-2.950.29691470.26842599X-RAY DIFFRACTION99.53
2.95-3.020.29131460.24792577X-RAY DIFFRACTION98.77
3.02-3.10.27581360.22722625X-RAY DIFFRACTION99.64
3.1-3.180.25211170.22232611X-RAY DIFFRACTION99.74
3.18-3.280.25051400.21732653X-RAY DIFFRACTION99.89
3.28-3.380.23631380.22072612X-RAY DIFFRACTION100
3.38-3.50.26231450.21652617X-RAY DIFFRACTION99.86
3.5-3.640.21881490.19752649X-RAY DIFFRACTION99.47
3.64-3.810.21671290.18652628X-RAY DIFFRACTION99.86
3.81-4.010.20251210.17422647X-RAY DIFFRACTION100
4.01-4.260.18581480.16582641X-RAY DIFFRACTION99.93
4.26-4.590.171390.14452653X-RAY DIFFRACTION99.61
4.59-5.050.1671540.14322676X-RAY DIFFRACTION99.51
5.05-5.780.17521530.16362673X-RAY DIFFRACTION100
5.78-7.280.21471380.20622740X-RAY DIFFRACTION99.58
7.28-55.810.17431530.18812816X-RAY DIFFRACTION98.31
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)
13.188069158670.265951782922-0.8797254527283.73014152775-3.053520360135.72186965043-0.06611158680360.2148326143060.3039329547810.2574068723510.0865571188612-0.113240236344-0.7371770939010.1963513955360.01316115600850.657717493737-0.01785787486550.105280927550.366771257733-0.0537664064090.50588124674616.797689061247.390835871849.5902762384
21.405879020781.128118491710.5095473339013.133555163180.7046331918751.57086930423-0.03166202582130.04468033734230.154875959886-0.02750645723410.07497701200370.0238010373893-0.1984660272690.124942691025-0.0168629203760.5205857387080.02336166147750.05095557326930.321014471715-0.01121677279690.34110314152413.808667429328.466226287148.2821029054
31.199382452262.07671374376-0.9423418074123.18216937716-1.649319467310.752724716540.00381148724723-0.183325386454-0.2014818074290.268774329564-0.0729892125591-0.1305848743670.1052557864320.04755554995710.06584112586770.6703500289110.05552956086420.03650365674710.3703856811640.00285139057710.3741198290741.783358277160.81456502131764.7918229314
41.425594102210.0886567711528-0.5037363265890.906321132199-0.5326113975451.30449811091-0.0537377385971-0.398684706305-0.09557010191650.185155478809-0.363324576966-0.2153606041730.4405309342580.434113867636-0.05881874755450.6953100828680.1048579515360.08257174113120.5822398459460.1934278077360.6082733697543.122676276246.214245893535.0771439932
5-0.0803373748284-0.540894344936-0.005839088425733.70308397971-2.102304940672.39246259223-0.0880052781849-0.534016823032-0.5558363658850.018502649945-0.379413319237-0.4528753500011.032788256532.180222654360.4844074645591.10095147440.5512580485380.2369298974571.585886986180.3985094170621.5201363985268.071610402845.582644988412.5492222494
61.33318355779-0.75235368544-0.9310449099021.014612795211.4852619441.417167689240.0361702591510.04422638875430.06264453761450.2528409549150.0899610590553-0.1815677743770.08727165326520.234359839550.0001991392013650.4038451618380.0608929526451-0.05732158638630.417108025385-0.04697433952710.36072755497919.5631336203-1.8537860935734.6463758743
71.948579375430.3488359594150.1701144185251.480064253670.5539642260161.38074067407-0.03050682508260.203315169591-0.07108224210730.406832068894-0.1454904062730.2781069133730.112698476261-0.244059387649-0.0002461528899520.4419716344670.007394126471220.0459640130880.432057578043-0.09416497509190.396803006489-0.84769499489-8.5815409636533.2912396345
88.50503713052-2.38225702606-2.803753429822.388035794961.364062830092.6984468017-0.0780470630344-0.354537706737-0.2486913973040.134793986180.0591476004574-0.08482530730880.3732141132430.2166368440150.04423677481850.3518593129230.0267981696467-0.05124877172210.406654553376-0.02697835233250.34982885284912.2396688069-31.61801700997.22546870166
93.17750806281-0.1094103722512.114307897132.41686770801-0.03497469950755.50937252765-0.09824924893720.0532776334906-0.0555180347146-0.0565879214750.168676538287-0.3256687485480.1138083645920.382289329238-0.085209035880.2493558716370.04902416303720.02806190864320.414730553807-0.08524567569850.45444620317520.017506341-17.86197664235.18210251888
100.614698509051-0.00229081666312-1.353847152720.301278611663-0.9830788071012.24613640303-0.1896377362340.1444280866480.0699393094016-0.1502589927060.0709924257178-0.1026303636550.413190161096-0.147320974384-1.33800224229E-50.480350823828-0.02264307111080.09959109667970.4704094528050.02580276682220.50970142539234.042253656356.201899311817.3586801265
112.85233326182-4.144660010040.702402666135.7693843271-1.485944677050.420727276609-0.1318169743520.0142445797317-1.01761612931-0.301110828924-0.101943797222-0.1564328676491.900638997781.340891835070.1001325861691.472161085530.4541833902920.3971403107790.8541040059730.05204090726171.0881796171357.844231789644.5048724014-0.710916043246
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain E and resid 1056:1107EF1056 - 11071 - 52
22chain E and resid 1108:1251EF1108 - 125153 - 196
33chain E and resid 1252:1423EF - H1252 - 1423197
44chain D and resid :113DE2 - 1131 - 122
55chain D and resid 114:DE114 - 209123 - 199
66chain B and resid :113BC2 - 1131 - 120
77chain A and resid :107AA1 - 1071 - 107
88chain A and resid 108:215AA108 - 215108 - 215
99chain B and resid 114:BC114 - 216121 - 223
1010chain C and resid :107CD2 - 1071 - 107
1111chain C and resid 108:CD108 - 207108 - 185

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