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 2.0 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
  • Primary Citation of Related Structures:  
    5JPN, 5JPM, 5JTW

  • 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-threading through low-resolution and/or weak electron density ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Complement C4-AA656Homo sapiensMutation(s): 0 
Gene Names: C4ACO4CPAMD2
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0L4 (Homo sapiens)
Explore P0C0L4 
Go to UniProtKB:  P0C0L4
PHAROS:  P0C0L4
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Complement C4-AB767Homo sapiensMutation(s): 1 
Gene Names: C4ACO4CPAMD2
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0L4 (Homo sapiens)
Explore P0C0L4 
Go to UniProtKB:  P0C0L4
PHAROS:  P0C0L4
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Complement C4-AC290Homo sapiensMutation(s): 0 
Gene Names: C4ACO4CPAMD2
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0L4 (Homo sapiens)
Explore P0C0L4 
Go to UniProtKB:  P0C0L4
PHAROS:  P0C0L4
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD3 N-Glycosylation Oligosaccharides Interaction
Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF, G5 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PBM
Query on PBM

Download Ideal Coordinates CCD File 
H [auth A], J [auth B], K [auth B], L [auth C]TRIMETHYL LEAD ION
C3 H9 Pb
SNBFOEGVGALPSE-UHFFFAOYSA-N
 Ligand Interaction
A2G
Query on A2G

Download Ideal Coordinates CCD File 
I [auth B]2-acetamido-2-deoxy-alpha-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-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  (Full details and data files)

  • 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
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary