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- PDB-4uu9: Crystal structure of the human c5a in complex with MEDI7814 a neu... -

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Basic information

Entry
Database: PDB / ID: 4uu9
TitleCrystal structure of the human c5a in complex with MEDI7814 a neutralising antibody
Components
  • (MEDI7814) x 2
  • COMPLEMENT C5
KeywordsIMMUNE SYSTEM / FV / COMPLEMENT SYSTEM
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
Anaphylotoxins (complement system) / Influenza Virus Matrix Protein; Chain A, domain 1 / : / 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 ...Anaphylotoxins (complement system) / Influenza Virus Matrix Protein; Chain A, domain 1 / : / 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 / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsColley, C. / Sridharan, S. / Dobson, C. / Popovic, B. / Debreczeni, J.E. / Hargreaves, D. / Edwards, B. / Brennan, J. / England, L. / Fung, S. ...Colley, C. / Sridharan, S. / Dobson, C. / Popovic, B. / Debreczeni, J.E. / Hargreaves, D. / Edwards, B. / Brennan, J. / England, L. / Fung, S. / An Eghobamien, L. / Sivars, U. / Woods, R. / Flavell, L. / Renshaw, G.J. / Wickson, K. / Wilkinson, T. / Davies, R. / Bonnell, J. / Warrener, P. / Howes, R. / Vaughan, T.
CitationJournal: MAbs / Year: 2018
Title: Structure and characterization of a high affinity C5a monoclonal antibody that blocks binding to C5aR1 and C5aR2 receptors.
Authors: Colley, C.S. / Popovic, B. / Sridharan, S. / Debreczeni, J.E. / Hargeaves, D. / Fung, M. / An, L.L. / Edwards, B. / Arnold, J. / England, E. / Eghobamien, L. / Sivars, U. / Flavell, L. / ...Authors: Colley, C.S. / Popovic, B. / Sridharan, S. / Debreczeni, J.E. / Hargeaves, D. / Fung, M. / An, L.L. / Edwards, B. / Arnold, J. / England, E. / Eghobamien, L. / Sivars, U. / Flavell, L. / Renshaw, J. / Wickson, K. / Warrener, P. / Zha, J. / Bonnell, J. / Woods, R. / Wilkinson, T. / Dobson, C. / Vaughan, T.J.
History
DepositionJul 25, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MEDI7814
B: MEDI7814
C: COMPLEMENT C5
D: COMPLEMENT C5
H: MEDI7814
L: MEDI7814
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,41310
Polymers67,0296
Non-polymers3844
Water5,423301
1
A: MEDI7814
B: MEDI7814
C: COMPLEMENT C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6114
Polymers33,5153
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-44.1 kcal/mol
Surface area13290 Å2
MethodPISA
2
D: COMPLEMENT C5
H: MEDI7814
L: MEDI7814
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8036
Polymers33,5153
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-61.3 kcal/mol
Surface area13550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.854, 117.472, 126.457
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody MEDI7814


Mass: 13508.873 Da / Num. of mol.: 2 / Fragment: VARIABLE DOMAIN HEAVY CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: HUMANISED ANTIBODY FRAGMENT / Production host: ESCHERICHIA COLI BL21 (bacteria)
#2: Antibody MEDI7814


Mass: 11629.880 Da / Num. of mol.: 2 / Fragment: VARIABLE DOMAIN LIGHT CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: HUMANISED ANTIBODY FRAGMENT / Production host: ESCHERICHIA COLI BL21 (bacteria)
#3: Protein COMPLEMENT C5 / C5A ANAPHYLATOXIN C5A / C3 AND PZP-LIKE ALPHA-2-MACROGLOBULIN DOMAIN-CONTAINING PROTEIN 4


Mass: 8375.754 Da / Num. of mol.: 2 / Fragment: C5A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: HUMANISED ANTIBODY FRAGMENT / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: P01031
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
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: 2.41 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growDetails: 20% PEG10K, 8% ETHYLENE GLYCOL, 100MM HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.12→126 Å / Num. obs: 48925 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 14.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 19
Reflection shellResolution: 2.12→2.24 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 8.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→86.07 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.54 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.20163 2472 5.1 %RANDOM
Rwork0.17456 ---
obs0.17595 46381 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.421 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.12→86.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4431 0 20 301 4752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194581
X-RAY DIFFRACTIONr_bond_other_d0.0010.024163
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.9476227
X-RAY DIFFRACTIONr_angle_other_deg0.7053.0029569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg19.4895.541629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.60223.036168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04215687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1191527
X-RAY DIFFRACTIONr_chiral_restr0.0720.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025511
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021096
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6331.4662391
X-RAY DIFFRACTIONr_mcbond_other0.6331.4662390
X-RAY DIFFRACTIONr_mcangle_it1.0662.192982
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0231.5722190
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.121→2.176 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 182 -
Rwork0.184 3403 -
obs--100 %
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)
12.30070.18550.80841.09930.28811.83180.02030.18830.0073-0.2642-0.01950.1422-0.0515-0.024-0.00080.08640.0055-0.01940.0223-0.00570.0302-28.3552-28.663238.9409
21.82930.5113-0.25331.5118-0.49641.90280.02370.02130.1956-0.0615-0.0412-0.1015-0.16910.12510.01740.0303-0.00650.01380.01080.00890.0402-10.881-18.695748.3697
36.7408-0.1661-3.11652.637-0.20513.127-0.0061-0.04760.2487-0.04930.04230.2061-0.2381-0.1654-0.03630.07190.0106-0.02640.0304-0.0050.035-40.2915-23.267559.7393
42.0148-0.5473-0.05513.44040.0991.3428-0.0338-0.13220.09420.046-0.1465-0.22490.04390.10710.18030.0697-0.011-0.01490.10960.08950.102-10.939616.378223.4763
52.6289-0.2254-0.13543.2867-0.46621.66350.03440.247-0.1831-0.2559-0.1374-0.51350.19060.30680.1030.15230.07380.09490.180.09160.1842-2.2228-3.722619.5132
65.892-1.3469-1.10193.4567-0.21724.2917-0.1605-0.3516-0.03740.63930.12240.22390.03-0.21130.03810.18550.00570.03070.1260.08560.1262-28.01054.924736.2688
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 107
2X-RAY DIFFRACTION2H1 - 112
3X-RAY DIFFRACTION3D0 - 65
4X-RAY DIFFRACTION4B3 - 108
5X-RAY DIFFRACTION5A1 - 112
6X-RAY DIFFRACTION6C0 - 64

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