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- PDB-4d9r: Inhibiting Alternative Pathway Complement Activation by Targeting... -

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Basic information

Entry
Database: PDB / ID: 4d9r
TitleInhibiting Alternative Pathway Complement Activation by Targeting the Exosite on Factor D
Components
  • Complement factor D
  • Fab heavy chain
  • Fab light chain
KeywordsHYDROLASE/IMMUNE SYSTEM / Factor D / complement / antibody / exosite / Fab / chymotrypsin / protease / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


complement factor D / IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Alternative complement activation / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / complement activation ...complement factor D / IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Alternative complement activation / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / complement activation / complement activation, alternative pathway / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / complement activation, classical pathway / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / serine-type peptidase activity / FCERI mediated Ca+2 mobilization / protein maturation / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / platelet alpha granule lumen / Regulation of Complement cascade / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / response to bacterium / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / Platelet degranulation / Interleukin-4 and Interleukin-13 signaling / secretory granule lumen / blood microparticle / adaptive immune response / Potential therapeutics for SARS / ficolin-1-rich granule lumen / immune response / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Trypsin-like serine proteases / Thrombin, subunit H / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulin-like fold / Peptidase S1, PA clan / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Complement factor D / Immunoglobulin kappa constant / Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsMurray, J.M. / Wiesmann, C.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Inhibiting alternative pathway complement activation by targeting the factor d exosite.
Authors: Katschke, K.J. / Wu, P. / Ganesan, R. / Kelley, R.F. / Mathieu, M.A. / Hass, P.E. / Murray, J. / Kirchhofer, D. / Wiesmann, C. / van Lookeren Campagne, M.
History
DepositionJan 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Database references
Revision 1.2May 2, 2012Group: Database references
Revision 1.3Sep 18, 2013Group: Database references
Revision 1.4Aug 2, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_residues / software
Revision 1.5Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 6, 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
A: Complement factor D
L: Fab light chain
H: Fab heavy chain
B: Complement factor D
E: Fab heavy chain
D: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,8008
Polymers141,7296
Non-polymers712
Water6,287349
1
A: Complement factor D
L: Fab light chain
H: Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)70,8643
Polymers70,8643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Complement factor D
E: Fab heavy chain
D: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9355
Polymers70,8643
Non-polymers712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.048, 132.048, 180.288
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Complement factor D / Adipsin / C3 convertase activator / Properdin factor D


Mass: 24438.807 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFD, DF, Factor D, PFD / Production host: Escherichia coli (E. coli) / References: UniProt: P00746, complement factor D
#2: Antibody Fab light chain


Mass: 23235.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGKC / Production host: Escherichia coli (E. coli) / References: UniProt: P01834
#3: Antibody Fab heavy chain


Mass: 23189.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01857
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl, 0.02 M NH4PO4, MPD 50.0% v/v, 0.01 M hexamine cobalt (III) chloride, pH 8.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 11, 2009
RadiationProtocol: SINGLE / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.42→25 Å / Num. all: 61198 / Num. obs: 60502 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 55.38 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.42-2.513.90.505199.5
2.51-2.6140.388199.8
2.61-2.7340.296199.8
2.73-2.8740.221199.6
2.87-3.054.10.154199.5
3.05-3.284.10.117199.2
3.28-3.6140.096198.8
3.61-4.1340.086198.1
4.13-5.240.077197.4
5.2-2540.067194.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.9.6refinement
PDB_EXTRACT3.1data extraction
BUSTER2.11.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HFD

1hfd


Resolution: 2.42→19.84 Å / Cor.coef. Fo:Fc: 0.9379 / Cor.coef. Fo:Fc free: 0.9174 / Occupancy max: 1 / Occupancy min: 0.3 / SU R Cruickshank DPI: 0.363 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 3064 5.08 %RANDOM
Rwork0.213 ---
obs0.2149 60373 98.65 %-
all-61198 --
Displacement parametersBiso mean: 53.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.9485 Å20 Å20 Å2
2--0.9485 Å20 Å2
3----1.8969 Å2
Refine analyzeLuzzati coordinate error obs: 0.331 Å
Refinement stepCycle: LAST / Resolution: 2.42→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9927 0 2 349 10278
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110179HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2513874HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3401SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes229HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1493HARMONIC5
X-RAY DIFFRACTIONt_it10179HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.37
X-RAY DIFFRACTIONt_other_torsion19.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1336SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11605SEMIHARMONIC4
LS refinement shellResolution: 2.42→2.48 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3222 215 4.84 %
Rwork0.2584 4230 -
all0.2614 4445 -
obs--98.65 %

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