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- PDB-4d9q: Inhibiting Alternative Pathway Complement Activation by Targeting... -

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Basic information

Entry
Database: PDB / ID: 4d9q
TitleInhibiting Alternative Pathway Complement Activation by Targeting the Exosite on Factor D
Components
  • (Anti-Factor D, ...) x 2
  • Factor D
KeywordsHYDROLASE/IMMUNE SYSTEM / Factor D / complement / antibody / exosite / Fab / chymotrypsin / protease / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


complement factor D / complement-dependent cytotoxicity / complement activation, alternative pathway / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding ...complement factor D / complement-dependent cytotoxicity / complement activation, alternative pathway / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / Notch signaling pathway / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / response to bacterium / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / blood microparticle / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / serine-type endopeptidase activity / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Complement factor D / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. ...Complement factor D / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Thrombin, subunit H / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Adipsin / Immunoglobulin heavy constant gamma 1 / Ig-like domain-containing protein
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 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 1.3Apr 2, 2014Group: Structure summary
Revision 1.4Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.5Sep 13, 2023Group: Data collection / Database references ...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_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Factor D
B: Factor D
D: Anti-Factor D, light chain
E: Anti-Factor D, heavy chain
H: Anti-Factor D, heavy chain
L: Anti-Factor D, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,36626
Polymers141,6996
Non-polymers1,66720
Water11,313628
1
A: Factor D
H: Anti-Factor D, heavy chain
L: Anti-Factor D, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,57912
Polymers70,8493
Non-polymers7309
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Factor D
D: Anti-Factor D, light chain
E: Anti-Factor D, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,78614
Polymers70,8493
Non-polymers93711
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Factor D
D: Anti-Factor D, light chain
E: Anti-Factor D, heavy chain
hetero molecules

A: Factor D
H: Anti-Factor D, heavy chain
L: Anti-Factor D, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,36626
Polymers141,6996
Non-polymers1,66720
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area15250 Å2
ΔGint-329 kcal/mol
Surface area53650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.330, 80.760, 142.630
Angle α, β, γ (deg.)90.00, 107.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Factor D /


Mass: 24630.061 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: pRK / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: F6YBP7

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Antibody , 2 types, 4 molecules DLEH

#2: Antibody Anti-Factor D, light chain


Mass: 23132.576 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TCD0
#3: Antibody Anti-Factor D, heavy chain


Mass: 23086.754 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

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Non-polymers , 4 types, 648 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 628 / Source method: isolated from a natural source / Formula: H2O

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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: 3.54 Å3/Da / Density % sol: 65.25 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 25% PEG 550 MME, 0.01 M zinc sulfate and 3% 6-aminohexanoic acid, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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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 WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.28→73.267 Å / Num. all: 90191 / Num. obs: 90191 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 44.55 Å2 / Rsym value: 0.047 / Net I/σ(I): 17.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.28-2.43.70.39920.399199.9
2.4-2.553.80.272.90.27199.9
2.55-2.733.80.1824.40.182199.9
2.73-2.953.80.11370.113199.9
2.95-3.233.80.06711.70.067199.9
3.23-3.613.80.04218.30.042199.8
3.61-4.163.70.0324.80.03199.6
4.16-5.13.70.0233.90.02199.6
5.1-7.213.70.0235.60.02199.7
7.21-73.2673.60.01442.60.014199.4

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
BUSTER-TNTBUSTER 2.11.2refinement
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
BUSTER2.11.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HFD

1hfd


Resolution: 2.28→33.38 Å / Cor.coef. Fo:Fc: 0.9195 / Cor.coef. Fo:Fc free: 0.899 / Occupancy max: 1 / Occupancy min: 0.3 / SU R Cruickshank DPI: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2301 4588 5.09 %RANDOM
Rwork0.1891 ---
obs0.1911 90153 99.63 %-
all-90191 --
Displacement parametersBiso mean: 49.03 Å2
Baniso -1Baniso -2Baniso -3
1-3.2059 Å20 Å213.5966 Å2
2--4.2886 Å20 Å2
3----7.4945 Å2
Refine analyzeLuzzati coordinate error obs: 0.268 Å
Refinement stepCycle: LAST / Resolution: 2.28→33.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9906 0 82 628 10616
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110201HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1713877HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3419SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes228HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1483HARMONIC5
X-RAY DIFFRACTIONt_it10201HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.51
X-RAY DIFFRACTIONt_other_torsion17.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1326SEMIHARMONIC5
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_contact11802SEMIHARMONIC4
LS refinement shellResolution: 2.28→2.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2537 345 5.29 %
Rwork0.2288 6173 -
all0.2301 6518 -
obs--99.63 %

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