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

  • 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 1.2 of the entry. See complete history


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: https://doi.org/10.1016/j.jbc.2021.100591
  • Primary Citation of Related Structures:  

  • 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 of AS in knock-in mice. To understand the context of this "Zurich" variant, an 8-amino acid appendage, we developed a construct of the WT α345 hexamer using the 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 12 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 features constitute bioactive sites, where pathogenic pathways converge that are linked to AS and GP, and, potentially, diabetic nephropathy. In Pedchenko et al., 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.

  • Organizational Affiliation

    Department of Biochemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Collagen alpha-3(IV) chain,Collagen alpha-4(IV) chain,Collagen alpha-5(IV) chain695Homo 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
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PE8

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TB [auth A]3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
Query on P6G

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C12 H26 O7
Query on 1PE

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C10 H22 O6
Query on PG4

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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]
C8 H18 O5
Query on PGE

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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]
C6 H14 O4
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]
C4 H10 O3
Query on EDO

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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]
C2 H6 O2
CL (Subject of Investigation/LOI)
Query on CL

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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]
Experimental Data & Validation

Experimental Data

  • 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
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
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description