6WKU

Twelve Chloride Ions Drive Assembly of Human alpha345 Collagen IV NC1 domain

  • Classification: STRUCTURAL PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2020-04-17 Released: 2021-04-07 
  • Deposition Author(s): Boudko, S.P., Hudson, B.G.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Collagen IV alpha 345 dysfunction in glomerular basement membrane diseases. II. Crystal structure of the alpha 345 hexamer.

Boudko, S.P.Bauer, R.Chetyrkin, S.V.Ivanov, S.Smith, J.Voziyan, P.A.Hudson, B.G.

(2021) J Biol Chem 296: 100591-100591

  • DOI: 10.1016/j.jbc.2021.100591
  • Primary Citation of Related Structures:  
    6WKU

  • PubMed Abstract: 
  • Our recent work identified a genetic variant of the α345 hexamer of the collagen IV scaffold that is present in patients with glomerular basement membrane diseases, Goodpasture's disease (GP) and Alport syndrome (AS), and phenocopies AS in knock-in mice (see Companion Paper I) ...

    Our recent work identified a genetic variant of the α345 hexamer of the collagen IV scaffold that is present in patients with glomerular basement membrane diseases, Goodpasture's disease (GP) and Alport syndrome (AS), and phenocopies AS in knock-in mice (see Companion Paper I). To understand the context of this "Zurich" variant, an 8-amino acid appendage, we developed a construct of the wild-type α345 hexamer using single-chain NC1 trimer technology, which allowed us to solve a crystal structure of this key connection module. The α345 hexamer structure revealed a ring of twelve chloride ions at the trimer-trimer interface, analogous to the collagen α121 hexamer, and the location of the 170 AS variants. The hexamer surface is marked by multiple pores and crevices that are potentially accessible to small molecules. Loop-crevice-loop (LCL) features constitute bioactive sites, where pathogenic pathways converge that are linked to Alport and GP diseases, and, potentially, diabetic nephropathy. In Companion Paper III, we demonstrate that these sites exhibit conformational plasticity, a dynamic property underlying assembly of bioactive sites and hexamer dysfunction. The α345 hexamer structure is a platform to decipher how variants cause AS, and how hypoepitopes can be triggered causing GP. Furthermore, the bioactive sites, along with the pores and crevices on the hexamer surface, are prospective targets for therapeutic interventions.


    Related Citations: 
    • Collagen IV alpha 345 dysfunction in glomerular basement membrane diseases. I. Discovery of a COL4A3 variant in familial Goodpasture's and Alport diseases.
      Pokidysheva, E.N., Seeger, H., Pedchenko, V., Chetyrkin, S., Bergmann, C., Abrahamson, D., Cui, Z.W., Delpire, E., Fervenza, F., Fidler, A.L., Fogo, A.B., Gaspert, A., Grohmann, M., Gross, O., Haddad, G., Harris, R.C., Kashtan, C., Kitching, A.R., Lorenzen, J.M., McAdoo, S., Pusey, C.D., Segelmark, M., Simmons, A., Voziyan, P.A., Wagner, T., Wuthrich, R.P., Zhao, M.H., Boudko, S.P., Kistler, A.D., Hudson, B.G.
      (2021) J Biol Chem --: 100590
    • Collagen IV alpha 345 dysfunction in glomerular basement membrane diseases. III. A functional framework for alpha 345 hexamer assembly.
      Pedchenko, V., Boudko, S.P., Barber, M., Mikhailova, T., Saus, J., Harmange, J.C., Hudson, B.G.
      (2021) J Biol Chem --: 100592

    Organizational Affiliation

    Dept. of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, USA; Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, USA; Aspirnaut, Vanderbilt University Medical Center, Nashville, TN, USA; Dept. of Pathology, Microbiology and Immunology, Vanderbilt University Med. Center, Nashville, TN, USA; Dept. of Biochemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Dept. of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Collagen alpha-3(IV) chain,Collagen alpha-4(IV) chain,Collagen alpha-5(IV) chainA695Homo sapiensMutation(s): 0 
Gene Names: COL4A3COL4A4COL4A5
UniProt & NIH Common Fund Data Resources
Find proteins for P53420 (Homo sapiens)
Explore P53420 
Go to UniProtKB:  P53420
PHAROS:  P53420
Find proteins for Q01955 (Homo sapiens)
Explore Q01955 
Go to UniProtKB:  Q01955
PHAROS:  Q01955
Find proteins for P29400 (Homo sapiens)
Explore P29400 
Go to UniProtKB:  P29400
PHAROS:  P29400
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP29400Q01955P53420
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PE8
Query on PE8

Download Ideal Coordinates CCD File 
TB [auth A]3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
GLZWNFNQMJAZGY-UHFFFAOYSA-N
 Ligand Interaction
P6G
Query on P6G

Download Ideal Coordinates CCD File 
H [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
V [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
AB [auth A],
BA [auth A],
BB [auth A],
CA [auth A],
EB [auth A],
AB [auth A],
BA [auth A],
BB [auth A],
CA [auth A],
EB [auth A],
M [auth A],
NB [auth A],
Q [auth A],
UB [auth A],
ZA [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
CB [auth A],
DA [auth A],
DB [auth A],
EA [auth A],
HA [auth A],
CB [auth A],
DA [auth A],
DB [auth A],
EA [auth A],
HA [auth A],
I [auth A],
J [auth A],
K [auth A],
KA [auth A],
L [auth A],
MA [auth A],
P [auth A],
PA [auth A],
QA [auth A],
QB [auth A],
S [auth A],
W [auth A],
WA [auth A],
Y [auth A],
ZB [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
DC [auth A],
FB [auth A],
GA [auth A],
GB [auth A],
HB [auth A],
DC [auth A],
FB [auth A],
GA [auth A],
GB [auth A],
HB [auth A],
IA [auth A],
JA [auth A],
JB [auth A],
JC [auth A],
KC [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
MC [auth A],
N [auth A],
NA [auth A],
O [auth A],
OA [auth A],
TA [auth A],
U [auth A],
UA [auth A],
VB [auth A],
X [auth A],
YB [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth A],
AC [auth A],
BC [auth A],
CC [auth A],
EC [auth A],
AA [auth A],
AC [auth A],
BC [auth A],
CC [auth A],
EC [auth A],
FA [auth A],
FC [auth A],
GC [auth A],
HC [auth A],
IB [auth A],
IC [auth A],
KB [auth A],
MB [auth A],
NC [auth A],
OB [auth A],
OC [auth A],
PB [auth A],
PC [auth A],
R [auth A],
RA [auth A],
RB [auth A],
SA [auth A],
SB [auth A],
T [auth A],
VA [auth A],
WB [auth A],
XA [auth A],
XB [auth A],
YA [auth A],
Z [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.42α = 90
b = 128.42β = 90
c = 104.71γ = 90
Software Package:
Software NamePurpose
MOSFLMdata processing
MOLREPphasing
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
pointlessdata scaling

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01DK018381

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2021-07-21
    Changes: Database references