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- PDB-7ad6: Crystal structure of human complement C5 in complex with the K92 ... -

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Basic information

Entry
Database: PDB / ID: 7ad6
TitleCrystal structure of human complement C5 in complex with the K92 bovine knob domain peptide.
Components
  • Complement C5
  • K92 knob domain
KeywordsIMMUNE SYSTEM / Complement C5 / C5 / ultralong / ultra-long / knob domain.
Function / homology
Function and homology information


Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / positive regulation of chemokine production ...Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / positive regulation of chemokine production / Peptide ligand-binding receptors / Regulation of Complement cascade / chemotaxis / G alpha (i) signalling events / killing of cells of another organism / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / inflammatory response / signaling receptor binding / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
: / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. ...: / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Alpha-2-macroglobulin / Macroglobulin domain / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold
Similarity search - Domain/homology
CYSTEINE / Complement C5
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMacpherson, A. / van den Elsen, J.M.H. / Schulze, M.E. / Birtley, J.R.
CitationJournal: Elife / Year: 2021
Title: The allosteric modulation of Complement C5 by knob domain peptides.
Authors: Macpherson, A. / Laabei, M. / Ahdash, Z. / Graewert, M.A. / Birtley, J.R. / Schulze, M.E. / Crennell, S. / Robinson, S.A. / Holmes, B. / Oleinikovas, V. / Nilsson, P.H. / Snowden, J. / ...Authors: Macpherson, A. / Laabei, M. / Ahdash, Z. / Graewert, M.A. / Birtley, J.R. / Schulze, M.E. / Crennell, S. / Robinson, S.A. / Holmes, B. / Oleinikovas, V. / Nilsson, P.H. / Snowden, J. / Ellis, V. / Mollnes, T.E. / Deane, C.M. / Svergun, D. / Lawson, A.D. / van den Elsen, J.M.
History
DepositionSep 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Structure summary / Category: audit_author
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 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
A: Complement C5
B: Complement C5
C: K92 knob domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)381,6319
Polymers380,6153
Non-polymers1,0166
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, 1:1 COMPLEX BETWEEN CHAINS A AND B AND THE PEPTIDE (chain C)., gel filtration, As part of a SEC MALLS experiment, the complex agreed with a A,B and C complex.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11590 Å2
ΔGint-32 kcal/mol
Surface area74810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.265, 104.285, 154.880
Angle α, β, γ (deg.)90.000, 124.899, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein / Protein/peptide / Sugars , 3 types, 4 molecules ABC

#1: Protein Complement C5 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 4


Mass: 188512.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01031
#2: Protein/peptide K92 knob domain


Mass: 3591.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 17 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H7NO2S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 1.78 Å3/Da / Density % sol: 30.79 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 0.1 M bicine/Trizma (pH 8.5), 10 % (w/v) PEG 8000, 20 % (v/v) ethylene glycol, 30 mM sodium fluoride, 30 mM sodium bromide and 30 mM sodium iodide.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.75→83.77 Å / Num. obs: 138366 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 78.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.01887 / Net I/σ(I): 28.79
Reflection shellResolution: 2.75→2.848 Å / Rmerge(I) obs: 0.2042 / Num. unique obs: 6877 / CC1/2: 0.924

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Processing

Software
NameVersionClassification
REFMAC5.5refinement
PHENIX1.18_3845refinement
xia2data reduction
Aimlessdata scaling
PHENIX1.18-3845-000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HCC

5hcc


Resolution: 2.75→83.77 Å / SU ML: 0.4522 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.339
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2535 3429 4.94 %
Rwork0.2194 65967 -
obs0.2211 138366 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.58 Å2
Refinement stepCycle: LAST / Resolution: 2.75→83.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13018 0 65 12 13095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001913360
X-RAY DIFFRACTIONf_angle_d0.5418122
X-RAY DIFFRACTIONf_chiral_restr0.04352068
X-RAY DIFFRACTIONf_plane_restr0.00362299
X-RAY DIFFRACTIONf_dihedral_angle_d18.04354902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.790.45771320.37222720X-RAY DIFFRACTION99.55
2.79-2.830.41321260.34492760X-RAY DIFFRACTION99.93
2.83-2.880.37211620.32582738X-RAY DIFFRACTION99.83
2.88-2.920.33961100.32282737X-RAY DIFFRACTION99.72
2.92-2.970.41521570.33242705X-RAY DIFFRACTION99.86
2.97-3.030.35581460.34872710X-RAY DIFFRACTION99.79
3.03-3.080.34371370.30962745X-RAY DIFFRACTION99.93
3.09-3.150.34731390.29632752X-RAY DIFFRACTION99.97
3.15-3.220.32911580.28952735X-RAY DIFFRACTION99.97
3.22-3.290.33831390.2722762X-RAY DIFFRACTION100
3.29-3.370.35221450.26562741X-RAY DIFFRACTION99.97
3.37-3.460.27871360.25062738X-RAY DIFFRACTION100
3.46-3.570.29421320.25462714X-RAY DIFFRACTION100
3.57-3.680.26331660.24692722X-RAY DIFFRACTION99.97
3.68-3.810.30861530.24272766X-RAY DIFFRACTION100
3.81-3.970.20961340.22582750X-RAY DIFFRACTION99.97
3.97-4.150.24581460.20522741X-RAY DIFFRACTION100
4.15-4.370.2361570.18952725X-RAY DIFFRACTION100
4.37-4.640.20311220.17482771X-RAY DIFFRACTION100
4.64-50.20911510.16252790X-RAY DIFFRACTION100
5-5.50.19711430.17392764X-RAY DIFFRACTION99.9
5.5-6.290.23731350.20392759X-RAY DIFFRACTION100
6.3-7.930.24421550.21792775X-RAY DIFFRACTION99.97
7.93-83.770.20151480.17772847X-RAY DIFFRACTION99.47
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)
10.4063710639290.01859895748540.3658076190930.478508336229-0.05671644246681.38911288128-0.0158582706284-0.252033489902-0.109173187071-0.1098481478660.150828791010.185927619485-0.126775646421-0.402699294335-0.1303436264820.603674481869-0.0350310423440.005712835160440.7005344561090.2133787132810.747376347987-32.3809119036-51.094149573235.663670767
22.312575358990.258738866486-0.291354748771.49762754864-0.481847991811.45214985116-0.1134234197460.08736515593350.0729102271282-0.1538140106150.1763007502550.00370120102267-0.3344845610520.0667210215683-0.06726679507180.673420985331-0.159950439156-0.05043623094360.4789676316360.03836784139110.415428652629-9.2687417099-33.648744340435.4921204919
30.762327973556-1.754463491221.279979173464.75196142349-3.96225823635.16917708903-0.232619506932-0.236284086794-0.3312119284970.4596770993540.1572323679550.229924987401-0.05894763755940.1106788816210.02226849440890.587427148260.1152619357790.170669808340.7088483821640.1936161143050.741769903382-19.9145709128-58.21145137771.0484913388
44.997313704650.870161435317-0.3605340597063.49800578931-1.757632065594.168125775410.3129128023850.558815406432-0.486102127238-0.553088190872-0.372643221753-0.129482346882-0.2166466357530.06160079155430.0875062500410.7274287060610.357095109284-0.01976412668930.644788209198-0.1048887230120.476520878224-29.6325647523-39.2810243196-32.2659326907
52.24084019422-0.886687372078-0.7116295520712.455105446530.3899851750835.35488516367-0.0375668459681-0.142476131451-0.190736121630.341596360229-0.0103900371795-0.001962519269250.1253594396670.07653253155970.06739320331360.593460910886-0.0729819502387-0.07389749890620.4879143511120.04556750478080.580402934646-27.8427991173-43.8952871294.40657404921
61.624334730060.100819292888-1.102625999750.91857943738-0.8997752735026.10090522720.1427848658460.292286422458-0.5968446593060.254318653018-0.03876816467640.511275272548-0.667254053227-1.02188643399-0.1152395610060.7554541968630.2023469763750.0248619432871.246942242690.05472045764020.996450427121-63.4386136592-40.24619252195.54982457242
73.35508316048-0.9355860762613.424417321573.60985534469-1.653916924295.665760322660.132978470072-0.136775787257-0.59116456393-0.633138053988-0.0407532787570.5559446221980.139316264009-1.52639423788-0.2704226471410.7044771236230.138980467734-0.2282309865651.22781355342-0.2747448545110.831540225556-50.9573190858-49.6019848892-31.3000068547
81.73557427319-0.2203318327830.4471658728830.232858221020.9082374082475.961584660060.1925839543240.243252314276-0.374444552636-0.07943589459390.1080097678790.3476794919621.02995021576-1.120278226-0.2671028221990.818022916628-0.150546769012-0.1220548304880.6862475349990.09014085077830.978038990919-38.750894554-61.70491128012.27297838116
94.2796128322-0.856439262891-2.38546658743.920533132560.215349089347.908383728250.118131260173-0.545229489726-7.78192653112E-50.0998084908527-0.226647216151-0.230350237287-1.36999337083-0.844553034640.02098031547210.795996826560.354400855307-0.2207868353031.14010755845-0.2751167277760.652877406734-46.0006081252-34.321196938-24.3081264846
101.036693002591.055540527820.4475796518691.47268854848-0.6845110496563.454822158330.2315913120680.12623470308-1.07156463825-0.09493576405780.2411780626090.04878152134530.7482923722521.16974580398-0.4407786021811.820759732250.4202545759860.2547748949111.97384195022-0.02100651001863.68029235747-24.805707743-58.670334011-31.255298651
111.82993486025-0.05648697750031.937555663440.00596998547689-0.06023744053922.05000305220.1073596675220.251281999742-0.694193466425-0.1528715519960.112204355905-0.1650465967130.1230904354570.34994278895-0.2592046932441.83675253268-0.4145000490670.3205681139991.963354065440.04818468850492.04310370228-32.130008515-57.7427466744-24.2679950906
120.509493098246-0.0109769604247-1.042110992230.09095361964940.361023891143.391929156330.08644926945240.396112691589-0.632226212218-0.448930506781-0.679817026831-0.9240061124020.5100957609510.6799855311160.515168783532.221592861161.21669623877-0.2363495957711.873925783880.2449141339632.2427158335-31.6446973848-55.6656150773-34.7211808269
134.06963932593-3.50067881593-0.7663054512437.53504421705-0.005898157720320.240380057670.1619949276170.0555239486213-1.91668601511-0.3831362625-0.5871130953341.103220574521.60623423246-0.8025377739080.4462345053881.972180514770.0826022969821-0.5367750533011.47307120252-0.5389455262152.43902972595-37.9374075081-59.2862383758-33.4946240821
140.0195028165263-0.02514875685540.009708924012270.123401840409-0.09006200875430.07241008431330.544251889317-0.502338103143-1.249458486481.08287229493-1.00207295045-0.6835118793590.988752429290.7283101678610.2909898725523.05315844445-0.149830059879-0.3131208986041.759144023630.699973325132.3478622992-29.8213761534-64.5308229039-29.8110695415
151.99990904823-4.68978468641-5.708385568222.000004497611.999926221471.99998773995-3.47593977102-9.61997437513-0.3816243847099.861221237445.99672215292-8.578901997890.859773855539-2.7848203276-2.505922152381.593816369430.126970592074-0.2499510089761.020516790110.1364130005811.50265356582-45.8747709667-30.899262752637.4273486133
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 684 through 1007 )AA684 - 10071 - 316
22chain 'A' and (resid 1008 through 1464 )AA1008 - 1464317 - 764
33chain 'A' and (resid 1465 through 1676 )AA1465 - 1676765 - 971
44chain 'B' and (resid 20 through 118 )BB20 - 1181 - 99
55chain 'B' and (resid 119 through 219 )BB119 - 219100 - 200
66chain 'B' and (resid 220 through 463 )BB220 - 463201 - 444
77chain 'B' and (resid 464 through 562 )BB464 - 562445 - 543
88chain 'B' and (resid 563 through 630 )BB563 - 630544 - 602
99chain 'B' and (resid 631 through 674 )BB631 - 674603 - 646
1010chain 'C' and (resid 2 through 10 )CC2 - 101 - 9
1111chain 'C' and (resid 11 through 19 )CC11 - 1910 - 18
1212chain 'C' and (resid 20 through 24 )CC20 - 2419 - 23
1313chain 'C' and (resid 25 through 29 )CC25 - 2924 - 28
1414chain 'C' and (resid 30 through 35 )CC30 - 3529 - 34
1515chain 'I' and (resid 1 through 1 )IK11

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