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- PDB-7ad7: Crystal structure of human complement C5 in complex with the K8 b... -

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Basic information

Entry
Database: PDB / ID: 7ad7
TitleCrystal structure of human complement C5 in complex with the K8 bovine knob domain peptide.
Components
  • Complement C5
  • K8 peptide
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 / ETHANOL / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / Complement C5
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 13, 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: Complement C5
A: Complement C5
C: K8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)384,30513
Polymers382,9863
Non-polymers1,32010
Water7,242402
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 area11340 Å2
ΔGint-41 kcal/mol
Surface area67690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.559, 161.695, 187.380
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 , 2 types, 3 molecules BAC

#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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C5, CPAMD4 / Production host: Homo sapiens (human) / References: UniProt: P01031
#2: Protein K8 peptide


Mass: 5961.453 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)

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Sugars , 1 types, 1 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 6 types, 411 molecules

#4: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MHA / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / N-(2-ACETAMIDO)IMINODIACETIC ACID


Mass: 190.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N2O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#7: 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
#8: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 1.61 Å3/Da / Density % sol: 23.75 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 0.1M ADA, 14% ethanol.

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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: 2.3→93.69 Å / Num. obs: 171135 / % possible obs: 99.83 % / Redundancy: 2 % / Biso Wilson estimate: 46.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.04257 / Net I/σ(I): 13.17
Reflection shellResolution: 2.3→2.382 Å / Rmerge(I) obs: 0.3613 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 10933 / CC1/2: 0.668 / % possible all: 99.82

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Processing

Software
NameVersionClassification
REFMAC5.5refinement
PHENIX1.18_3845refinement
xia2data reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CU7

3cu7


Resolution: 2.3→93.69 Å / SU ML: 0.2806 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.1592
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2336 5585 5.05 %
Rwork0.202 104905 -
obs0.2036 171135 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.09 Å2
Refinement stepCycle: LAST / Resolution: 2.3→93.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11568 0 86 402 12056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003211954
X-RAY DIFFRACTIONf_angle_d0.627116228
X-RAY DIFFRACTIONf_chiral_restr0.0471841
X-RAY DIFFRACTIONf_plane_restr0.00362061
X-RAY DIFFRACTIONf_dihedral_angle_d17.40264357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.37251700.30113487X-RAY DIFFRACTION99.89
2.33-2.350.34261770.29713435X-RAY DIFFRACTION99.67
2.35-2.380.29951780.27553465X-RAY DIFFRACTION99.89
2.38-2.410.30061650.27563520X-RAY DIFFRACTION99.81
2.41-2.440.28671590.2663436X-RAY DIFFRACTION99.69
2.44-2.480.30151940.26853448X-RAY DIFFRACTION99.78
2.48-2.510.30511700.26813448X-RAY DIFFRACTION99.61
2.51-2.550.31052080.27033478X-RAY DIFFRACTION99.78
2.55-2.590.34171730.27613417X-RAY DIFFRACTION99.72
2.59-2.630.30861820.26263508X-RAY DIFFRACTION99.81
2.63-2.680.30262060.25883395X-RAY DIFFRACTION99.92
2.68-2.730.2731920.25013486X-RAY DIFFRACTION99.84
2.73-2.780.31021830.24613454X-RAY DIFFRACTION99.73
2.78-2.840.24842180.22943453X-RAY DIFFRACTION99.86
2.84-2.90.27531940.2233461X-RAY DIFFRACTION99.89
2.9-2.970.28481660.22913497X-RAY DIFFRACTION99.78
2.97-3.040.28121860.22393474X-RAY DIFFRACTION99.89
3.04-3.120.2772070.23663466X-RAY DIFFRACTION99.95
3.12-3.210.27791860.23063486X-RAY DIFFRACTION99.97
3.21-3.320.23582060.21513460X-RAY DIFFRACTION100
3.32-3.440.22531800.20323534X-RAY DIFFRACTION99.97
3.44-3.570.21061660.19173514X-RAY DIFFRACTION99.92
3.57-3.740.24351890.18823487X-RAY DIFFRACTION99.86
3.74-3.930.20371800.18593543X-RAY DIFFRACTION99.97
3.93-4.180.20831980.17413514X-RAY DIFFRACTION100
4.18-4.50.18491720.15333568X-RAY DIFFRACTION99.97
4.5-4.950.17192130.14883510X-RAY DIFFRACTION99.97
4.96-5.670.20161780.16013586X-RAY DIFFRACTION99.97
5.67-7.150.20982050.19043592X-RAY DIFFRACTION99.95
7.15-93.690.20391840.19783783X-RAY DIFFRACTION99.4
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)
19.445470997011.30105772027-6.1072814436.51757796028-1.389545020178.792261219980.2013151085261.179916379830.426720077601-0.3462821492520.09895967793270.288376994111-0.182307744655-0.501782736269-0.3358858162610.3580884384330.01115028724150.006324550869850.3408174393420.104927703610.27984659862746.791391745245.01142726640.802376776006
21.909558923210.588798224616-0.3079096094522.2885499074-2.222788444022.214418010930.3038354832940.157147763049-0.5091063750990.0252580530325-0.08467661497430.614355522204-0.0109960197219-0.334152950885-0.1948545463490.778091936176-0.0949185151337-0.2928776492150.995823903310.2338867676251.0741467259832.480946894452.4275144829-7.5172212484
37.43157271495-3.485907915051.682671865494.606481182974.312108774959.138583448980.21097835524-1.376758337051.37773427421-1.796162631020.07123125421332.00398951009-0.820418760028-1.70350719717-0.293345883580.7716623671060.3148403568210.03657692750081.51579904249-0.1450484301331.3651992838938.647206975753.920165389-13.7469563347
41.99998730742-8.331400015667.155164389117.12849800265-1.443911418186.019713528680.7160624288421.691690865611.71908616533-0.574705079579-0.8384854775920.1133335987050.09888643334410.9524411592340.1265799982261.52550631039-0.05633458877930.0629248817441.56815775746-0.1828249898351.5364037790154.806683613953.620014100328.8300495064
55.118981980830.8671915948621.173002004793.97155781180.1053020119945.146056280970.219961217638-0.1403157399370.1144452001170.0477080495919-0.1550617227870.0926311921427-0.0365428884814-0.393520005443-0.04597317677370.217326894644-0.006301234641610.06459876853970.373092600652-0.009109024640240.3206027255628.451094973545.694775280791.8224188665
61.92420551345-0.847238419357-0.6129084641661.68080411702-0.02105558233392.57173227847-0.1110405328610.228568156947-0.12991402044-0.1600790389030.03536142308760.07490797449890.2355365296040.05895866790830.06372146565480.350218334117-0.06357667275730.008664411752570.567683868321-0.1000443804710.29663577876140.628308447836.878631769957.8500882139
71.571760714612.39019247940.9807142990593.911915648972.61770667143.63788644822-0.4263095165810.944948584886-0.127775022331-0.819114676750.870928271114-0.450075197015-0.2121023011720.937168958003-0.3863502393510.789294109972-0.0270602808430.1923531767761.03620324709-0.2145344296390.74201694980869.051802893555.662179790944.019204286
82.472436079120.506421290987-1.340755704421.164598633851.230984005366.55607234537-0.01160464487280.198390200187-0.0866679339272-0.210933910561-0.0277109559473-0.0877711304662-0.2296229815270.330888128794-0.005275363457420.405883214616-0.01002169761790.1002287830630.280570682666-0.05393734334830.68729182399965.030965420265.901851969.3997040451
92.28409954637-0.235165921878-0.005653593814447.00392023441.740594496993.841329621260.0703155154338-0.3563255905920.4313160858170.5486374272730.035162762027-0.398778047679-0.09715014221160.261439342529-0.1147307797850.243058971957-0.0461909458205-0.004752770731880.395414302611-0.02668734198270.39069282603450.074476135752.855831620996.7067583521
102.14500031419-1.36818552854-3.114709782081.610251642323.325374185278.40595333116-0.09321663962190.07637177310.0660253208578-0.1833143737260.35444046248-0.7260353203440.5206223299131.21155355843-0.2748642354610.500491311040.1723311336670.1085104257220.845732868986-0.006678476225680.54723665273564.017824477727.11283239767.6082799606
110.1753832238290.02931573850320.02038603128160.4689291415670.5626003016391.45558821327-0.04755286325860.2214238782060.0764010529655-0.0152495496325-0.06599007428560.191825588894-0.00121766788728-0.05109585278470.1066309639230.3783628892690.007629763176330.1010314948330.5134162948560.02650259271840.50116950966646.774316768445.839830204177.4583857228
120.3152326401320.138100666384-0.234845676559-0.1836070387520.5119529523621.40054608172-0.114735319943-0.1677340831440.1391409249870.009302340887560.04166823343010.0420341602152-0.1530175950340.3791678319620.1079322016580.5129003148940.001759461642180.06670796409810.6034663069530.0201107978740.5764563367363.677039694734.296674727237.5012266303
131.792995312230.259690007585-0.2082845458370.983987361808-0.08730103945210.888918988329-0.0896456643672-0.236260077712-0.2143445918070.1213474276880.0116556412856-0.08681905082110.02414196706190.04426467766940.07847942416210.2848673116380.04059322292670.01280675531570.3275882108480.03522757426060.23961607709732.976168007626.10896139921.8015834651
144.069473781375.302686079814.085097746646.902515843075.327550493374.11667213286-0.7697808300030.8882093739760.670426382503-1.24544198960.4799863889081.74117871362-1.44286927839-0.4235973601860.2982842834970.612436320822-0.0127348074901-0.1187229923720.69050056862-0.003190208184010.612589210738.127416724450.6048812862-5.83560427668
154.57030480277-0.5015242119942.779305993350.231506837630.4882864508825.592798809420.0008955230120670.437686049512-0.04750846707050.0411058081378-0.01156132828990.141589086991-0.1401538555670.242470006672-0.01998896743710.417942439812-0.05672123392480.01551640044380.4004890156710.0002522438812650.39216196215645.232561328441.4788557265-5.23987220581
163.128893003752.236824544454.272899286772.286487366913.019059138237.50306005693-0.1115375845230.629302157545-2.09925738112-0.5396183921440.40685752143-2.15348840456-0.1104589819910.499101055912-0.3313366712180.333732743646-0.07181923470930.05033543950860.5602783031170.008903492721580.63309187876558.381052839737.21899295190.452750358342
173.24261665069-1.528250223811.230126394264.125026290993.775632330995.954306644860.006725655311920.119112994759-0.437259398372-0.5327465241310.1258807541350.7093409640130.100220334024-0.313293341873-0.1131103401370.385870031289-0.05447166147240.03173451046870.4953006743210.05413554521650.30447292748945.236472456739.3556234684-4.5045455877
185.31725726858-0.902012616226-3.005300483575.59759682147-4.818250221536.915507532720.150127032364-0.3246389290962.18926564522-0.7955771297230.02922952647290.235376318488-0.6811099591190.470259766998-0.1132517754790.583232674816-0.0976031696442-0.05049120866490.416187684417-0.02368989761780.65109759387150.273086730252.4212971987-1.12343499619
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 36 through 45 )CC36 - 4537 - 47
22chain 'C' and (resid 46 through 50 )CC46 - 5048 - 52
33chain 'C' and (resid 51 through 52 )CC51 - 5253 - 54
44chain 'M' and (resid 1 through 1 )MO11
55chain 'B' and (resid 20 through 118 )BA20 - 1181 - 99
66chain 'B' and (resid 119 through 219 )BA119 - 219100 - 200
77chain 'B' and (resid 220 through 293 )BA220 - 293201 - 274
88chain 'B' and (resid 294 through 455 )BA294 - 455275 - 436
99chain 'B' and (resid 456 through 562 )BA456 - 562437 - 543
1010chain 'B' and (resid 563 through 588 )BA563 - 588544 - 571
1111chain 'B' and (resid 589 through 671 )BA589 - 671572 - 637
1212chain 'A' and (resid 683 through 929 )AB683 - 9291 - 212
1313chain 'A' and (resid 930 through 1513 )AB930 - 1513213 - 785
1414chain 'C' and (resid 1 through 6 )CC1 - 61 - 6
1515chain 'C' and (resid 7 through 15 )CC7 - 157 - 15
1616chain 'C' and (resid 16 through 22 )CC16 - 2216 - 23
1717chain 'C' and (resid 23 through 30 )CC23 - 3024 - 31
1818chain 'C' and (resid 31 through 35 )CC31 - 3532 - 36

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