4YD9

Crystal structure of squid hemocyanin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.275 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Crystal Structure of the 3.8-MDa Respiratory Supermolecule Hemocyanin at 3.0 angstrom Resolution

Gai, Z.Matsuno, A.Kato, K.Kato, S.Khan, M.R.I.Shimizu, T.Yoshioka, T.Kato, Y.Kishimura, H.Kanno, G.Miyabe, Y.Terada, T.Tanaka, Y.Yao, M.

(2015) Structure 23: 2204-2212

  • DOI: https://doi.org/10.1016/j.str.2015.09.008
  • Primary Citation of Related Structures:  
    4YD9

  • PubMed Abstract: 

    Molluscan hemocyanin, a copper-containing oxygen transporter, is one of the largest known proteins. Although molluscan hemocyanins are currently applied as immunotherapeutic agents, their precise structure has not been determined because of their enormous size. Here, we have determined the first X-ray crystal structure of intact molluscan hemocyanin. The structure unveiled the architecture of the 3.8-MDa supermolecule composed of homologous functional units (FUs), wherein the dimers of FUs hierarchically associated to form the entire cylindrical decamer. Most of the specific inter-FU interactions were localized at narrow regions in the FU dimers, suggesting that rigid FU dimers formed by specific interactions assemble with flexibility. Furthermore, the roles of carbohydrates in assembly and allosteric effect, and conserved sulfur-containing residues in copper incorporation, were revealed. The precise structural information obtained in this study will accelerate our understanding of the molecular basis of hemocyanin and its future applications.


  • Organizational Affiliation

    Laboratory of X-Ray Structural Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
hemocyanin
A,
BA [auth b],
D,
G,
J,
M,
P,
S,
V,
Y
2,000Todarodes pacificusMutation(s): 0 
Entity Groups  
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
hemocyanin
B,
CA [auth c],
E,
H,
K,
N,
Q,
T,
W,
Z
920Todarodes pacificusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
hemocyanin394Todarodes pacificusMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AC [auth QA],
BB [auth 1],
BC [auth RA],
CB [auth 2],
EA [auth e],
AC [auth QA],
BB [auth 1],
BC [auth RA],
CB [auth 2],
EA [auth e],
EB [auth 4],
FA [auth f],
GB [auth 6],
HB [auth 7],
IA [auth i],
IB [auth 8],
JA [auth j],
JB [auth 9],
LB [auth BA],
MA [auth m],
NA [auth n],
OA [auth o],
PA [auth p],
QA [auth q],
RB [auth HA],
SA [auth s],
SB [auth IA],
TA [auth t],
TB [auth JA],
UA [auth u],
VA [auth v],
WB [auth MA],
XA [auth x],
YB [auth OA]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
GA [auth g],
KB [auth AA],
LA [auth l],
PB [auth FA],
UB [auth KA],
GA [auth g],
KB [auth AA],
LA [auth l],
PB [auth FA],
UB [auth KA],
ZB [auth PA]
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
DB [auth 3],
FB [auth 5],
HA [auth h],
KA [auth k],
MB [auth CA],
DB [auth 3],
FB [auth 5],
HA [auth h],
KA [auth k],
MB [auth CA],
NB [auth DA],
OB [auth EA],
QB [auth GA],
RA [auth r],
VB [auth LA],
WA [auth w],
XB [auth NA],
YA [auth y]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 7
MoleculeChains 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-glucopyranoseZA [auth z]5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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-glucopyranoseAB [auth 0]4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CUO
Query on CUO

Download Ideal Coordinates CCD File 
AD [auth H]
AE [auth S]
AF [auth b]
BD [auth I]
BE [auth S]
AD [auth H],
AE [auth S],
AF [auth b],
BD [auth I],
BE [auth S],
BF [auth c],
CC [auth A],
CD [auth I],
CE [auth S],
CF [auth c],
DC [auth A],
DD [auth J],
DE [auth S],
DF [auth d],
EC [auth A],
ED [auth J],
EE [auth T],
FC [auth A],
FD [auth J],
FE [auth T],
GC [auth A],
GD [auth J],
GE [auth U],
HC [auth B],
HD [auth J],
HE [auth V],
IC [auth B],
ID [auth K],
IE [auth V],
JC [auth C],
JD [auth K],
JE [auth V],
KC [auth C],
KD [auth M],
KE [auth V],
LC [auth D],
LD [auth M],
LE [auth V],
MC [auth D],
MD [auth M],
ME [auth W],
NC [auth D],
ND [auth M],
NE [auth W],
OC [auth D],
OD [auth M],
OE [auth X],
PC [auth D],
PD [auth N],
PE [auth Y],
QC [auth E],
QD [auth N],
QE [auth Y],
RC [auth E],
RD [auth O],
RE [auth Y],
SC [auth F],
SD [auth P],
SE [auth Y],
TC [auth F],
TD [auth P],
TE [auth Y],
UC [auth G],
UD [auth P],
UE [auth Z],
VC [auth G],
VD [auth P],
VE [auth Z],
WC [auth G],
WD [auth P],
WE [auth b],
XC [auth G],
XD [auth Q],
XE [auth b],
YC [auth G],
YD [auth Q],
YE [auth b],
ZC [auth H],
ZD [auth S],
ZE [auth b]
CU2-O2 CLUSTER
Cu2 O2
PCGDDKBKPXANNY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.275 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.37α = 90
b = 538.66β = 104.09
c = 310.92γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references
  • Version 1.2: 2020-02-05
    Changes: Data collection, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary