Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 141.61 kDa 
• Atom Count: 9984 
• Modelled Residue Count: 1224 
• Deposited Residue Count: 1224 
• Unique protein chains: 1

1LNL

Structure of deoxygenated hemocyanin from Rapana thomasiana

• DOI: 10.2210/pdb1LNL/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Rapana venosa
• Mutation(s): No 


• Deposited: 2002-05-03 Released: 2003-06-03 
• Deposition Author(s): Perbandt, M., Guthoehrlein, E.W., Rypniewski, W., Idakieva, K., Stoeva, S., Voelter, W., Genov, N., Betzel, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.288 
• R-Value Work: 0.248 
• R-Value Observed: 0.250 

Literature

The structure of a functional unit from the wall of a gastropod hemocyanin offers a possible mechanism for cooperativity

Perbandt, M., Guthoehrlein, E.W., Rypniewski, W., Idakieva, K., Stoeva, S., Voelter, W., Genov, N., Betzel, C.

(2003) Biochemistry 42: 6341-6346

• PubMed: 12767214 
• DOI: 10.1021/bi020672x
• Primary Citation of Related Structures:  
  1LNL


• PubMed Abstract: 
  

Structure-function relationships in a molluscan hemocyanin have been investigated by determining the crystal structure of the Rapana thomasiana (gastropod) hemocyanin functional unit RtH2e in deoxygenated form at 3.38 A resolution. This is the first X-ray structure of an unit from the wall of the molluscan hemocyanin cylinder. The crystal structure of RtH2e demonstrates molecular self-assembly of six identical molecules forming a regular hexameric cylinder. This suggests how the functional units are ordered in the wall of the native molluscan hemocyanins. The molecular arrangement is stabilized by specific protomer-to-protomer interactions, which are probably typical for the functional units building the wall of the cylinders. A molecular mechanism for cooperative dioxygen binding in molluscan hemocyanins is proposed on the basis of the molecular interactions between the protomers. In particular, the deoxygenated RtH2e structure reveals a tunnel leading from two opposite sides of the molecule to the active site. The tunnel represents a possible entrance pathway for dioxygen molecules. No such tunnels have been observed in the crystal structure of the oxy-Odg, a functional unit from the Octopus dofleini (cephalopod) hemocyanin in oxygenated form.

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Organizational Affiliation: 

Institute of Biochemistry and Molecular Biology I, University Hospital Hamburg-Eppendorf, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hemocyanin	A, B, C	408	Rapana venosa	Mutation(s): 0
UniProt
Find proteins for P83040 (Rapana venosa) Explore P83040  Go to UniProtKB:  P83040

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	D [auth A], K [auth C], L [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CU	E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B], M [auth C], N [auth C], O [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.288 
• R-Value Work: 0.248 
• R-Value Observed: 0.250 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.486	α = 90
b = 105.486	β = 90
c = 374.988	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2002-05-03 
• Released Date: 2003-06-03 
Deposition Author(s): Perbandt, M., Guthoehrlein, E.W., Rypniewski, W., Idakieva, K., Stoeva, S., Voelter, W., Genov, N., Betzel, C.

Revision History  

• Version 1.0: 2003-06-03
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2018-07-04
  Changes: Advisory, Data collection, Derived calculations
• Version 1.4: 2019-11-20
  Changes: Advisory, Derived calculations
• Version 1.5: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary