5JPN

Structure of human complement C4 rebuilt using iMDFF

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2016-05-03 Released: 2016-08-10 
  • Deposition Author(s): Croll, T.I., Andersen, G.R.
  • Funding Organization(s): Aarhus University Research Foundation, Danish Science Research Council for Nature and Universe

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in:4FXK


Literature

Re-evaluation of low-resolution crystal structures via interactive molecular-dynamics flexible fitting (iMDFF): a case study in complement C4.

Croll, T.I.Andersen, G.R.

(2016) Acta Crystallogr D Struct Biol 72: 1006-1016

  • DOI: 10.1107/S2059798316012201
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • While the rapid proliferation of high-resolution structures in the Protein Data Bank provides a rich set of templates for starting models, it remains the case that a great many structures both past and present are built at least in part by hand-threa ...

    While the rapid proliferation of high-resolution structures in the Protein Data Bank provides a rich set of templates for starting models, it remains the case that a great many structures both past and present are built at least in part by hand-threading through low-resolution and/or weak electron density. With current model-building tools this task can be challenging, and the de facto standard for acceptable error rates (in the form of atomic clashes and unfavourable backbone and side-chain conformations) in structures based on data with dmax not exceeding 3.5 Å reflects this. When combined with other factors such as model bias, these residual errors can conspire to make more serious errors in the protein fold difficult or impossible to detect. The three recently published 3.6-4.2 Å resolution structures of complement C4 (PDB entries 4fxg, 4fxk and 4xam) rank in the top quartile of structures of comparable resolution both in terms of Rfree and MolProbity score, yet, as shown here, contain register errors in six β-strands. By applying a molecular-dynamics force field that explicitly models interatomic forces and hence excludes most physically impossible conformations, the recently developed interactive molecular-dynamics flexible fitting (iMDFF) approach significantly reduces the complexity of the conformational space to be searched during manual rebuilding. This substantially improves the rate of detection and correction of register errors, and allows user-guided model building in maps with a resolution lower than 3.5 Å to converge to solutions with a stereochemical quality comparable to atomic resolution structures. Here, iMDFF has been used to individually correct and re-refine these three structures to MolProbity scores of <1.7, and strategies for working with such challenging data sets are suggested. Notably, the improved model allowed the resolution for complement C4b to be extended from 4.2 to 3.5 Å as demonstrated by paired refinement.


    Related Citations: 
    • Structural basis for activation of the complement system by component C4 cleavage.
      Kidmose, R.T., Laursen, N.S., Dobo, J., Kjaer, T.R., Sirotkina, S., Yatime, L., Sottrup-Jensen, L., Thiel, S., Gal, P., Andersen, G.R.
      (2012) Proc Natl Acad Sci U S A 109: 15425

    Organizational Affiliation

    Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Complement C4-A
A
656Homo sapiensMutation(s): 0 
Gene Names: C4ACO4CPAMD2
Find proteins for P0C0L4 (Homo sapiens)
Go to UniProtKB:  P0C0L4
NIH Common Fund Data Resources
PHAROS  P0C0L4
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Complement C4-A
B
767Homo sapiensMutation(s): 1 
Gene Names: C4ACO4CPAMD2
Find proteins for P0C0L4 (Homo sapiens)
Go to UniProtKB:  P0C0L4
NIH Common Fund Data Resources
PHAROS  P0C0L4
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Complement C4-A
C
290Homo sapiensMutation(s): 0 
Gene Names: C4ACO4CPAMD2
Find proteins for P0C0L4 (Homo sapiens)
Go to UniProtKB:  P0C0L4
NIH Common Fund Data Resources
PHAROS  P0C0L4
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PBM
Query on PBM

Download CCD File 
A, B, C
TRIMETHYL LEAD ION
C3 H9 Pb
SNBFOEGVGALPSE-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
A2G
Query on A2G

Download CCD File 
B
N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
 Ligand Interaction
BMA
Query on BMA

Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MAN
Query on MAN

Download CCD File 
B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.45α = 90
b = 103.31β = 90
c = 256.03γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Aarhus University Research FoundationDenmark--
Danish Science Research Council for Nature and UniverseDenmark--

Revision History 

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-09-14
    Changes: Database references
  • Version 1.2: 2018-09-19
    Changes: Data collection
  • Version 1.3: 2018-11-21
    Changes: Data collection
  • Version 1.4: 2019-01-23
    Changes: Advisory, Data collection, Derived calculations