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- PDB-7b26: CirpA1 in complex with pseudo-monomeric Properdin lacking TSR2-3 -

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Basic information

Entry
Database: PDB / ID: 7b26
TitleCirpA1 in complex with pseudo-monomeric Properdin lacking TSR2-3
Components
  • (Properdin) x 2
  • CirpA1
KeywordsIMMUNOSUPPRESSANT / Inhibitor / Complement / Tick / Complex
Function / homology
Function and homology information


cytoplasmic side of Golgi membrane / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / Alternative complement activation / Activation of C3 and C5 / complement activation / complement activation, alternative pathway / Regulation of Complement cascade / positive regulation of immune response ...cytoplasmic side of Golgi membrane / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / Alternative complement activation / Activation of C3 and C5 / complement activation / complement activation, alternative pathway / Regulation of Complement cascade / positive regulation of immune response / specific granule lumen / tertiary granule lumen / defense response to bacterium / immune response / endoplasmic reticulum lumen / Neutrophil degranulation / extracellular space / extracellular region
Similarity search - Function
: / : / Thrombospondin type 1 repeat / CFP-like, C-terminal thrombospondin type 1 domain / : / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat
Similarity search - Domain/homology
alpha-D-mannopyranose / Properdin
Similarity search - Component
Biological speciesHomo sapiens (human)
Rhipicephalus pulchellus (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsLea, S.M. / Johnson, S. / Braunger, K.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Wellcome Trust100298 United Kingdom
Wellcome Trust209194 United Kingdom
Wellcome Trust219477 United Kingdom
Medical Research Council (MRC, United Kingdom)S021264 United Kingdom
European Molecular Biology Organization (EMBO)ALTF 554-2019 United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Structure and function of a family of tick-derived complement inhibitors targeting properdin.
Authors: Braunger, K. / Ahn, J. / Jore, M.M. / Johnson, S. / Tang, T.T.L. / Pedersen, D.V. / Andersen, G.R. / Lea, S.M.
History
DepositionNov 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: 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 / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Jul 24, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Properdin
A: Properdin
C: CirpA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,34913
Polymers62,4023
Non-polymers1,94810
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-1 kcal/mol
Surface area27070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.310, 54.512, 70.581
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Properdin / Complement factor P


Mass: 27484.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFP, PFC / Production host: Homo sapiens (human) / References: UniProt: P27918
#2: Protein Properdin / Complement factor P / FP head fragment (TB-TSR1)


Mass: 14485.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFP, PFC / Production host: Homo sapiens (human) / References: UniProt: P27918
#3: Protein CirpA1


Mass: 20431.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhipicephalus pulchellus (arthropod) / Production host: Escherichia coli (E. coli)
#4: Polysaccharide beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3LFucpa1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1221m-1a_1-5][a2122h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-L-Fucp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.15 M Potassium thiocyanate, 0.1 M Tris, pH 7.5, 18 % w/v PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91589 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91589 Å / Relative weight: 1
ReflectionResolution: 2.842→83.155 Å / Num. obs: 7444 / % possible obs: 89.4 % / Redundancy: 10.7 % / Biso Wilson estimate: 63.54 Å2 / CC1/2: 0.994 / Net I/σ(I): 6.1
Reflection shellResolution: 2.842→3.277 Å / Rmerge(I) obs: 1.82 / Num. unique obs: 372 / CC1/2: 0.599

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
PHENIX1.18rc4_3812refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CirpA1, 6S08

6s08


Resolution: 3.4→24.71 Å / SU ML: 0.3361 / Cross valid method: FREE R-VALUE / Phase error: 26.4346
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2741 336 4.93 %
Rwork0.2292 6486 -
obs0.2315 6822 73.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.12 Å2
Refinement stepCycle: LAST / Resolution: 3.4→24.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3560 0 120 0 3680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00443780
X-RAY DIFFRACTIONf_angle_d0.87445134
X-RAY DIFFRACTIONf_chiral_restr0.0503559
X-RAY DIFFRACTIONf_plane_restr0.0051654
X-RAY DIFFRACTIONf_dihedral_angle_d13.2031491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-4.280.32341050.26672221X-RAY DIFFRACTION51.06
4.28-24.710.25922310.21584265X-RAY DIFFRACTION94.53
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)
11.99185967388-0.0581389616219-0.2648294009421.950944958610.529108692552.99192877967-0.1456707300540.4527007807910.430069612270.05715494845030.06162380661860.256678946197-0.490062461978-0.3185818718630.02408233378180.511420597155-0.1038901654810.004695543238310.2845008023720.06034596725520.8192394284162.963037693674.7694503398545.1591134186
21.337771977180.0872119634892-1.241463754060.9023222740480.3372475939691.242519256220.239054747680.9023472438460.431727104014-0.498383567489-0.2110880851150.811079930240.1540446620030.449904647259-0.04881536214430.6208979180070.538660901569-0.02336592303291.178007413340.5451403812610.80804578085340.7880749242-0.41976971843512.641883076
31.552098658121.31832121734-0.2858295937091.800155524211.631822814896.601511367160.008992207765430.04656709587160.352803976029-0.2502116410320.2532768088670.0631981972722-1.033028298020.757835983249-0.278047407760.5205171811470.2190345423960.05348996264730.815806371862-0.06449703483340.60763235956560.72534669783.2163401166425.159359858
47.59556085997-7.156206091122.570127410872.0230370355-2.109776623474.87312460990.6645704003210.01267402891740.8788459749990.1490322826950.0320081071113-0.39344819094-0.613329319061-0.262188011722-0.4738884408860.5985127004250.001642870248860.2977172331970.6954445371120.2117183777950.63737128359959.2587712062-0.95118883914114.8753852386
53.19717504402-0.764400204941-1.322581998131.62328851274-0.402123136663.324982870220.4416774191520.0493983771307-0.01601266605910.516894729034-0.460176930501-0.5930098899490.08890601255020.483435368046-0.05689303038520.7576372671370.140077927965-0.08147770540221.10336851614-0.2945407228830.33464381540762.9513856767-0.71743821753239.7610113023
69.506143564594.52418438579-2.929984878223.82867920364-0.1939385575597.279494224090.204583374781-0.4993956289570.0325163571437-0.555690329842-0.485136294977-0.456713309888-1.181756129410.04230120668160.327687463030.634901935957-0.03454788831590.05555539890520.270684541801-0.1346844404971.0054583701322.79722483514.9134797083645.1858271203
70.00498915811833-0.005789717230490.004924006418520.1896626336240.1229007949170.0877877750346-0.128818682919-0.1976967467620.0139774338446-0.05352428331010.01911780184490.0739246815240.121772178669-0.2130360810280.107219245229-0.277513690424-0.9647286917310.373643146822-0.501397131827-0.3438482284591.26891154414.04109236950.53213363497447.5288024134
82.960901969480.5223782001233.790814359432.418997783241.9307908818.15420817227-0.0823442106733-0.373530098069-0.7601552741940.04488860515470.122861120518-0.5171559225920.35367046820.0311025437597-0.1079711136720.301388452955-0.002988183701580.005562129898440.2825753678920.01851572793570.78184913708520.0515481531-1.6463494745844.1337180377
98.005313929172.34626977912-3.7254438118.6336357828-5.136831065964.46525610516-0.8055531166270.3816779174280.280602489589-0.9842776656730.153325442615-0.172800721905-0.4043630875420.1592622777630.5487014271630.5431739385610.126438260640.03799369327670.8169425394480.1360397863990.36053549730927.4193003695-0.083734071216438.4420754698
100.665589936254-0.637806852385-1.203812762760.913325161423-0.261159376389.69633121519-0.8104963230180.475681093616-0.3094098258190.3477953843730.7720510327410.195649650124-0.8800037723540.959602385810.008833966113940.4286932447940.09691818425550.0142729994670.791540495133-0.09633942311350.52796349254543.38309093047.6463628067542.9865388661
119.45048305551-4.565687401732.546002492777.854485437021.406945339118.750468453610.859580285586-2.148020288022.134526061140.5779091710420.899882729844-1.0917042793-1.956528177972.38031473833-1.544097772141.003255603040.0875112407089-0.04328636464491.76765099336-0.7483238940991.122871390259.554738614913.343364471354.0428029078
122.114107764083.45292835312.55098659493.01497127154-0.04286338115534.39014742583-0.1443729010411.19503516102-0.514733638979-0.1110449118670.58441129256-0.126601701518-0.03053719895060.783949579383-0.4023635539690.4375201067510.1049199915980.09183006546960.554698592857-0.09245207438350.49410960133640.7336204079-0.47179794860342.1086618065
130.005261446290410.07271880306750.06502284038970.9195875535870.8401283231250.758544044144-0.2776365466520.05983573153210.407113569270.1691472574940.0579554056655-0.511973603707-0.02999923300870.2720700610110.1868561907760.6577135226390.335635096199-0.2916609284412.686301635030.178631220212.4984132382361.670389696318.134512533650.2932677855
146.95509240143.02569919723-0.1199514329292.07558782008-6.509221624034.579608501540.6234000632160.887976422795-1.06880342363-0.840853396080.574679916455-0.2468119086090.500694433083-0.374815254475-0.9617174849910.7875461170910.1169851836820.03225075824830.647171271942-0.1244691436910.59907216316365.8578693072-19.2394478299-2.23754679907
155.1544897135-6.31927435004-3.76796879579.818144893726.846953982848.699330022070.214995069060.5913900983090.129806389588-0.6703671026510.202319897065-0.591096075726-0.4091283563470.825258841922-0.2716782855860.951338003276-0.2284932430190.1407342131870.64808535586-0.07950507738580.33124325119676.1193185647-6.40897708279-6.75418823203
162.526246963370.361300177367-1.938582705573.15819695370.01424709642836.12464449636-0.2355659290830.248729062383-1.13277328861-0.07559911281380.194878009441-0.8544509301560.05223066818910.798234006128-0.06894868549280.6111566193230.3595521245860.1249690963780.891897384595-0.1396015697150.99913035838177.1182332693-19.82316600680.915261797452
177.218933805343.35857985157-3.682956473154.25382164828-2.873246378676.78937102740.730644836861.087951249880.315845458079-0.253863306996-0.02218585545630.410246736244-0.370421942977-0.641308498229-0.7475827791580.4845454457950.1120274433770.003106490038620.321830342542-0.01232472786340.57378621853868.8071445209-17.29522837067.82891469163
187.2547294715-0.120119882002-2.557835601184.96814298303-2.840028087245.95006195006-0.1445012372290.374096732605-1.60442653148-0.1624173776070.0822233914746-0.2090668724730.27497179362-0.8358931244170.1163681261910.4107656235890.07173161802080.1025679387690.323665585069-0.01088182803480.51433303245767.0341829255-14.13287027682.40671368611
195.28126282144-4.67956351769-1.264032799875.462845457980.04862452986166.38036091593-0.222475730387-0.2245344645520.66059416767-0.490941222801-0.0799248799282-0.533666905373-0.8800460694710.3688617384510.1425684652490.3753794294170.08267289393630.1068085730640.155116875982-0.0869883601660.77924739143169.7695680724-6.338632906281.86225534607
206.24590409939-4.603155207361.866025036675.26883604567-2.444377495633.957592792910.4840704976861.30467150756-0.515029443707-1.3666922574-0.205671609453-0.8663490425831.81077943355-0.626940450566-0.283189624391.13912943483-0.07300035401190.09255563034920.884052777059-0.2818996142010.75743724252665.0217491111-18.5131822734-15.3465207806
210.4030958612620.4686554974670.5330399524976.991817515472.070692148432.79452273808-0.04277408970830.478146796849-0.0308783469725-0.5244170989290.08299724203651.00767224452-0.2286389148420.200263587622-0.08061051790261.619329275140.3784990339950.1013198883940.6698263874440.5085860495460.28324377599858.014490193-4.5963598345-7.75348379858
225.78477164788-2.27553889052-0.6216035550638.160232553532.572917360853.916153238290.1780047447851.27306925023-0.465489139929-0.5074234375490.481752769423-0.323523921663-0.0633062849040.442557045743-0.2535880222660.9802654609470.35967297560.4531129424341.246311537220.3031394395320.5399667876373.5644493915-9.23364050547-12.9537256637
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 260 through 317 )BA260 - 3171 - 48
22chain 'B' and (resid 318 through 372 )BA318 - 37249 - 103
33chain 'B' and (resid 373 through 428 )BA373 - 428104 - 156
44chain 'B' and (resid 429 through 438 )BA429 - 438157 - 166
55chain 'B' and (resid 439 through 464 )BA439 - 464167 - 192
66chain 'A' and (resid 28 through 44 )AK28 - 441 - 17
77chain 'A' and (resid 45 through 52 )AK45 - 5218 - 25
88chain 'A' and (resid 53 through 71 )AK53 - 7126 - 44
99chain 'A' and (resid 72 through 79 )AK72 - 7945 - 52
1010chain 'A' and (resid 80 through 89 )AK80 - 8953 - 62
1111chain 'A' and (resid 90 through 95 )AK90 - 9563 - 68
1212chain 'A' and (resid 96 through 127 )AK96 - 12769 - 100
1313chain 'A' and (resid 128 through 133 )AK128 - 133101 - 106
1414chain 'C' and (resid 48 through 66 )CC48 - 661 - 19
1515chain 'C' and (resid 67 through 75 )CC67 - 7520 - 28
1616chain 'C' and (resid 76 through 97 )CC76 - 9729 - 50
1717chain 'C' and (resid 98 through 119 )CC98 - 11951 - 72
1818chain 'C' and (resid 120 through 143 )CC120 - 14373 - 96
1919chain 'C' and (resid 144 through 165 )CC144 - 16597 - 118
2020chain 'C' and (resid 166 through 176 )CC166 - 176119 - 129
2121chain 'C' and (resid 177 through 190 )CC177 - 190130 - 143
2222chain 'C' and (resid 191 through 203 )CC191 - 203144 - 156

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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

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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

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