[English] 日本語
Yorodumi
- PDB-7rah: Adenylate cyclase toxin RTX domain fragment bound to M1H5 Fab and... -

+
Open data


ID or keywords:

Loading...

-
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 / RTX toxin determinant A / Haemolysin-type calcium binding-related / Haemolysin-type calcium binding protein related domain / : / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit ...RTX, pore-forming domain / N-terminal domain in RTX protein / RTX toxin determinant A / Haemolysin-type calcium binding-related / Haemolysin-type calcium binding protein related domain / : / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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)

-
Non-polymers , 3 types, 208 molecules

#6: Chemical ChemComp-PO4 / PHOSPHATE ION


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


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

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more