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- PDB-5i5k: Structure of complement C5 in complex with eculizumab -

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Basic information

Entry
Database: PDB / ID: 5i5k
TitleStructure of complement C5 in complex with eculizumab
Components
  • Complement C5
  • Eculizumab heavy chain (variable domain)
  • Eculizumab light chain (variable domain)
KeywordsIMMUNE SYSTEM / Complement / Fab
Function / homology
Function and homology information


Terminal pathway of complement / membrane attack complex / negative regulation of macrophage chemotaxis / Activation of C3 and C5 / complement activation, GZMK pathway / other organism cell membrane / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production ...Terminal pathway of complement / membrane attack complex / negative regulation of macrophage chemotaxis / Activation of C3 and C5 / complement activation, GZMK pathway / other organism cell membrane / 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 / Regulation of Complement cascade / Peptide ligand-binding receptors / chemotaxis / killing of cells of another organism / G alpha (i) signalling events / cell surface receptor signaling pathway / inflammatory response / G protein-coupled receptor signaling pathway / signaling receptor binding / : / 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 / 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 / Tissue inhibitor of metalloproteinases-like, OB-fold / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsSchatz-Jakobsen, J.A. / Andersen, G.R.
CitationJournal: J Immunol. / Year: 2016
Title: Structural Basis for Eculizumab-Mediated Inhibition of the Complement Terminal Pathway.
Authors: Schatz-Jakobsen, J.A. / Zhang, Y. / Johnson, K. / Neill, A. / Sheridan, D. / Andersen, G.R.
History
DepositionFeb 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jun 29, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Complement C5
H: Eculizumab heavy chain (variable domain)
L: Eculizumab light chain (variable domain)
A: Complement C5
X: Eculizumab heavy chain (variable domain)
Y: Eculizumab light chain (variable domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)474,2288
Polymers473,0556
Non-polymers1,1732
Water00
1
B: Complement C5
H: Eculizumab heavy chain (variable domain)
L: Eculizumab light chain (variable domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,1144
Polymers236,5283
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Complement C5
X: Eculizumab heavy chain (variable domain)
Y: Eculizumab light chain (variable domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,1144
Polymers236,5283
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)197.704, 269.321, 202.824
Angle α, β, γ (deg.)90.00, 98.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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: Antibody Eculizumab heavy chain (variable domain)


Mass: 24860.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Eculizumab light chain (variable domain)


Mass: 23154.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
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: 5.64 Å3/Da / Density % sol: 78.2 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Imidazole pH 6.2 4% v/v Tacsimate pH 7 8% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 4.2→49.8 Å / Num. obs: 76073 / % possible obs: 99.6 % / Redundancy: 4.9 % / Rsym value: 0.166 / Net I/σ(I): 6.28
Reflection shellHighest resolution: 4.2 Å / Redundancy: 5.01 % / Mean I/σ(I) obs: 1.29 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KMT, 3PVM

4kmt

3pvm
PDB Unreleased entry


Resolution: 4.2→49.795 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2436 1865 2.45 %
Rwork0.2045 --
obs0.2055 76073 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.2→49.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32452 0 78 0 32530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00333282
X-RAY DIFFRACTIONf_angle_d0.64145218
X-RAY DIFFRACTIONf_dihedral_angle_d10.37420052
X-RAY DIFFRACTIONf_chiral_restr0.0455150
X-RAY DIFFRACTIONf_plane_restr0.0045738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2-4.31350.33581430.32015687X-RAY DIFFRACTION100
4.3135-4.44040.32921430.30735672X-RAY DIFFRACTION100
4.4404-4.58360.351430.28875704X-RAY DIFFRACTION100
4.5836-4.74730.34321440.27255714X-RAY DIFFRACTION100
4.7473-4.93720.32251430.26545696X-RAY DIFFRACTION99
4.9372-5.16170.28641420.23125653X-RAY DIFFRACTION100
5.1617-5.43350.26281440.22285714X-RAY DIFFRACTION100
5.4335-5.77340.28361440.22235722X-RAY DIFFRACTION100
5.7734-6.21840.27481430.21575715X-RAY DIFFRACTION100
6.2184-6.84280.23551440.20535701X-RAY DIFFRACTION100
6.8428-7.82970.25011450.18295746X-RAY DIFFRACTION100
7.8297-9.8520.17221430.15375719X-RAY DIFFRACTION100
9.852-49.79830.18741440.16165765X-RAY DIFFRACTION99
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)
11.88021.0083-1.27442.443-0.9291.1086-0.1122.0171-0.7777-0.98581.0143-0.9781.33722.66330.08931.5383-0.21390.03865.2491-0.42742.217846.419782.711834.6804
21.91921.08830.85553.04882.84183.685-0.59493.78880.02340.22920.8936-0.0874-0.46661.06740.00221.6432-0.25760.03763.2998-0.29531.81839.929172.842442.0811
31.2027-0.7604-1.84851.61251.75782.45150.01521.59540.9981-1.61760.17030.08330.4953-0.327702.663-0.8105-0.71043.46251.01462.2688-14.993693.18823.7668
40.2971-0.7745-0.27271.4510.75580.1456-0.72981.07111.047-1.54760.82080.3868-1.16970.08230.00042.9705-1.5073-0.53015.95181.39572.721419.5281103.44069.8054
52.3752-0.0012-1.76353.1961-0.55661.3745-1.58541.99561.8647-1.9620.82320.6276-0.81061.7126-0.33092.8808-1.73170.23157.12160.54332.08838.214688.079912.636
62.48692.00460.46262.38971.64061.1247-0.89170.8513-0.1413-0.53591.2697-0.44260.33220.953601.8436-0.17080.26323.5923-0.61631.71184.160863.075224.5316
72.6095-0.1065-1.10842.00321.02514.6689-0.4402-0.3016-1.2742-0.269-0.2035-0.02560.59471.6796-0.00052.1256-0.1146-0.26562.7797-0.03121.8026-30.22753.929925.4987
81.4337-1.72630.12511.8276-0.0896-0.0092-0.61183.82751.41830.01610.9499-0.0468-0.35571.08770.00222.6337-0.8450.00274.55610.55782.082324.967788.740627.1753
94.2044-0.3177-0.2361-0.05910.34043.01070.44390.8677-1.12010.0982-0.1239-0.18350.6679-0.09930.00022.4578-0.0708-0.01561.4266-0.03312.1414-19.065841.498165.9448
103.4033-1.72-1.39735.79020.09063.7375-0.03640.1247-0.00920.26970.0480.2402-0.04620.5210.00011.5394-0.1476-0.12931.3459-0.02021.3045-8.694767.664673.1274
114.250.740.60785.59822.50393.50090.34290.69330.39560.1995-0.29250.26540.41920.0907-01.7228-0.2001-0.07561.69160.14811.5093-33.366472.639554.7223
122.5171-2.3915-0.2732.24660.99551.17241.22242.73471.3379-0.9417-0.76850.0213-0.35060.61050.00072.16660.18620.17872.78120.65892.3987-26.383898.126646.7868
131.7035-0.5497-1.76710.11940.5371.56241.4306-0.9894-1.04442.49710.59370.9587-0.6265-1.6659-0.0024.1503-0.63530.02393.60080.27773.8026-56.216338.685653.3085
143.1274-1.26342.25632.7482-0.21463.518-0.1014-0.20640.1311-1.0776-0.2610.1102-0.37940.2102-0.00041.6361-0.0296-0.33962.1279-0.1082.108769.3023104.3467133.8584
150.02230.0396-0.12990.0888-0.32750.2969-1.1575-4.41481.88650.98670.3883-0.6587-2.0733-1.17760.00332.74130.5159-1.00624.9418-0.78613.329390.7756107.6213163.8024
160.7254-0.5561.14260.5326-0.74571.6232-0.5733-1.5528-0.2362-0.4150.4851-0.95271.39881.74160.00021.74850.3197-0.12082.47170.03582.859783.42987.9934131.1116
170.06470.15220.24331.21831.71082.2809-0.6429-1.56251.00632.7381-1.0630.53562.7427-2.5781-0.06393.16440.2456-0.22675.0468-0.14622.64790.009292.1838167.0681
182.37260.6547-1.83231.6911-1.25092.70050.26720.6053-0.2937-1.2958-0.5180.45680.88660.79610.00032.3748-0.12060.00281.4977-0.30911.678422.519635.282275.5519
194.7651-0.50580.13792.9564-0.24641.9839-0.1060.4396-0.0292-0.7254-0.2992-0.1209-0.0994-0.3508-01.6535-0.22130.1711.2054-0.05461.906932.2371.658483.1756
204.79661.6931-3.42792.265-0.56953.6283-0.41230.2514-0.22990.19520.3089-0.37470.25370.140501.59170.1967-0.12251.5892-0.07911.692828.057281.4136118.3565
212.5223-0.38160.03953.90921.7324.73020.0686-0.1356-0.1866-0.13790.1115-0.2669-0.37980.10480.00021.72790.02980.09151.30180.07411.685922.155842.8727116.6889
222.44930.2487-0.41584.7864-1.72332.75860.338-0.6589-0.0882-0.3345-0.4469-0.99060.81450.9286-0.00031.80980.10120.03960.9951-0.05531.947430.645930.627297.5595
233.69631.34731.73932.64390.49410.72890.3224-0.3549-0.66030.867-0.0698-0.41290.2315-0.04420.00011.56160.1749-0.04621.4840.00832.115350.328769.59793.3101
242.2873-1.83762.20446.2915-1.40462.08550.03-0.82590.1524-0.55580.7422-0.86840.403-0.0977-0.00051.6376-0.19850.04291.7122-0.10342.060862.1517101.1343106.0784
251.28451.2708-1.37361.4546-0.74081.60890.2134-0.0472-0.3157-0.5891-0.4822-0.9002-0.776-0.3658-0.0011.92870.08570.15991.6149-0.01781.893224.284249.380294.1844
261.1354-0.23581.09762.9790.53883.1052-0.43290.65680.0240.41020.19530.10540.1730.08310.00011.849-0.25470.39562.01690.082.150652.1106111.760164.8671
273.945-1.4879-0.19443.5846-0.10553.89110.06380.67330.5203-0.16480.15720.05520.1078-0.25420.00011.5923-0.1301-0.09111.45980.22821.578524.364103.283967.0735
284.43061.00741.26061.3470.81782.8279-0.2108-0.31340.49060.33630.04280.1954-0.2165-0.20.00011.7612-0.08830.05651.328-0.01312.021632.3065115.396594.6979
290.978-0.8665-0.43990.87770.09460.8999-0.8356-0.72620.19120.9949-0.1074-0.08450.4055-0.6575-0.00012.60680.01920.16212.10890.23652.41612.9786102.2486109.2576
303.03780.09290.00445.2699-1.94434.05070.15520.53690.3348-0.81230.5769-0.9104-0.54860.5409-0.00021.8211-0.07330.33941.2477-0.17532.256965.007140.484393.665
312.25841.88360.53921.6471-0.20142.79640.439-1.03340.73860.47560.84831.41141.4762-1.41620.00032.6896-0.5189-0.08933.1210.41091.9217-46.894457.83152.0379
320.8772-1.1434-0.05794.6151-0.25250.0148-0.151.6550.0522-2.2380.3429-0.2820.9325-4.30070.3822.9613-0.9709-0.81485.520.09081.8971-62.700950.8366-31.0962
332.6457-1.1444-1.42871.7758-1.07222.4139-0.52060.7581-0.51-2.37910.4469-0.0021.7571.5590.00092.9106-0.12950.0762.10790.05731.758-30.93148.0456-9.3747
344.62460.3699-0.13930.7338-0.44890.45970.23541.99052.2658-0.03330.24820.7851.8827-3.08830.06183.2691-0.3531-0.56334.82860.10761.3746-50.520657.4187-38.088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1resid 19:120 and chain a
2X-RAY DIFFRACTION2resid 121:224 and chain a
3X-RAY DIFFRACTION3resid 225:349 and chain a
4X-RAY DIFFRACTION4resid 350:460 and chain a
5X-RAY DIFFRACTION5resid 461:566 and chain a
6X-RAY DIFFRACTION6(resid 567:606 or resid 760:821) and chain a
7X-RAY DIFFRACTION7resid 822:930 and chain a
8X-RAY DIFFRACTION8resid 607:673 and chain a
9X-RAY DIFFRACTION9(resid 931:983 or resid 1305:1367) and chain a
10X-RAY DIFFRACTION10resid 984:1304 and chain a
11X-RAY DIFFRACTION11resid 1368:1520 and chain a
12X-RAY DIFFRACTION12resid 676:759 and chain a
13X-RAY DIFFRACTION13resid 1525:1700 and chain a
14X-RAY DIFFRACTION14chain h and resid 1:120
15X-RAY DIFFRACTION15chain h and resid 121:230
16X-RAY DIFFRACTION16chain l and resid 1:105
17X-RAY DIFFRACTION17chain l and resid 106:230
18X-RAY DIFFRACTION18resid 19:120 and chain b
19X-RAY DIFFRACTION19resid 121:224 and chain b
20X-RAY DIFFRACTION20resid 225:349 and chain b
21X-RAY DIFFRACTION21resid 350:460 and chain b
22X-RAY DIFFRACTION22resid 461:566 and chain b
23X-RAY DIFFRACTION23(resid 567:606 or resid 760:821) and chain b
24X-RAY DIFFRACTION24resid 822:930 and chain b
25X-RAY DIFFRACTION25resid 607:673 and chain b
26X-RAY DIFFRACTION26(resid 931:983 or resid 1305:1367) and chain b
27X-RAY DIFFRACTION27resid 984:1304 and chain B
28X-RAY DIFFRACTION28resid 1368:1520 and chain B
29X-RAY DIFFRACTION29resid 676:759 and chain B
30X-RAY DIFFRACTION30resid 1525:1700 and chain B
31X-RAY DIFFRACTION31chain X and resid 1:120
32X-RAY DIFFRACTION32chain X and resid 121:230
33X-RAY DIFFRACTION33chain Y and resid 1:105
34X-RAY DIFFRACTION34chain Y and resid 106:230

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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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