[English] 日本語
Yorodumi
- PDB-4d9r: Inhibiting Alternative Pathway Complement Activation by Targeting... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4d9r
TitleInhibiting Alternative Pathway Complement Activation by Targeting the Exosite on Factor D
Components
  • Complement factor DFactor D
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
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 / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / Alternative complement activation / CD22 mediated BCR regulation / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation ...complement factor D / IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / Alternative complement activation / CD22 mediated BCR regulation / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / antibody-dependent cellular cytotoxicity / Fc epsilon receptor (FCERI) signaling / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / complement activation, classical pathway / antigen binding / serine-type peptidase activity / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / platelet alpha granule lumen / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / response to bacterium / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Platelet degranulation / antibacterial humoral response / blood microparticle / secretory granule lumen / Interleukin-4 and Interleukin-13 signaling / ficolin-1-rich granule lumen / Potential therapeutics for SARS / adaptive immune response / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...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. / Trypsin-like serine protease / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

#1: Protein Complement factor D / 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 / Fragment antigen-binding


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 / Fragment antigen-binding


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 / Chloride


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


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more