1YHU

Crystal structure of Riftia pachyptila C1 hemoglobin reveals novel assembly of 24 subunits.

• PDB DOI:  https://doi.org/10.2210/pdb1YHU/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Riftia pachyptila
• Mutation(s): No 


• Deposited: 2005-01-10 Released: 2005-02-08 
• Deposition Author(s): Flores, J.F., Fisher, C.R., Carney, S.L., Green, B.N., Freytag, J.K., Schaeffer, S.W., Royer, W.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.271 
• R-Value Work: 0.243 
• R-Value Observed: 0.243 

Literature

Sulfide binding is mediated by zinc ions discovered in the crystal structure of a hydrothermal vent tubeworm hemoglobin.

Flores, J.F., Fisher, C.R., Carney, S.L., Green, B.N., Freytag, J.K., Schaeffer, S.W., Royer Jr, W.E.

(2005) Proc Natl Acad Sci U S A 102: 2713-2718

• PubMed: 15710902 
• DOI: https://doi.org/10.1073/pnas.0407455102
• Primary Citation of Related Structures:  
  1YHU


• PubMed Abstract: 
  

Key to the remarkable ability of vestimentiferan tubeworms to thrive in the harsh conditions of hydrothermal vents are hemoglobins that permit the sequestration and delivery of hydrogen sulfide and oxygen to chemoautotrophic bacteria. Here, we demonstrate that zinc ions, not free cysteine residues, bind sulfide in vestimentiferan hemoglobins. The crystal structure of the C1 hemoglobin from the hydrothermal vent tubeworm Riftia pachyptila has been determined to 3.15 A and revealed the unexpected presence of 12 tightly bound Zn(2+) ions near the threefold axes of this D(3) symmetric hollow sphere. Chelation experiments on R. pachyptila whole-coelomic fluid and purified hemoglobins reveal a role for Zn(2+) ions in sulfide binding. Free cysteine residues, previously proposed as sulfide-binding sites in vestimentiferan hemoglobins, are found buried in surprisingly hydrophobic pockets below the surface of the R. pachyptila C1 molecule, suggesting that access of these residues to environmental sulfide is restricted. Attempts to reduce the sulfide-binding capacities of R. pachyptila hemoglobins by addition of a thiol inhibitor were also unsuccessful. These findings challenge the currently accepted paradigm of annelid hemoglobin evolution and adaptation to reducing environments.

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Organizational Affiliation: 

Department of Biology, Pennsylvania State University, University Park, PA 16802, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Hetero 24-mer - A6B6C6D6 Pseudo Symmetry: Dihedral - D3  (3D View)
Pseudo Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 396.75 kDa 
• Atom Count: 27,804 
• Modelled Residue Count: 3,516 
• Deposited Residue Count: 3,516 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hemoglobin A1 chain	A, E, I, M, Q, U	145	Riftia pachyptila	Mutation(s): 0  Gene Names: hbA1
UniProt
Find proteins for Q8IFK4 (Riftia pachyptila) Explore Q8IFK4  Go to UniProtKB:  Q8IFK4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Giant hemoglobins B chain	B, F, J, N, R, V	144	Riftia pachyptila	Mutation(s): 0
UniProt
Find proteins for P80592 (Riftia pachyptila) Explore P80592  Go to UniProtKB:  P80592

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
hemoglobin B1a chain	C, G, K, O, S, W	148	Riftia pachyptila	Mutation(s): 0  Gene Names: hbB1a
UniProt
Find proteins for Q8IFK2 (Riftia pachyptila) Explore Q8IFK2  Go to UniProtKB:  Q8IFK2

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
hemoglobin B2 chain	D, H, L, P, T, X	149	Riftia pachyptila	Mutation(s): 0  Gene Names: hbB2
UniProt
Find proteins for Q8IFJ9 (Riftia pachyptila) Explore Q8IFJ9  Go to UniProtKB:  Q8IFJ9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	AB [auth L], AC [auth V], CA [auth B], CB [auth M], CC [auth W], EA [auth C], EC [auth X], GA [auth D], GB [auth N], IA [auth E], IB [auth O], KB [auth P], MA [auth F], MB [auth Q], OA [auth G], QA [auth H], QB [auth R], SA [auth I], SB [auth S], UB [auth T], WA [auth J], WB [auth U], Y [auth A], YA [auth K]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
ZN	AA [auth B], BA [auth B], EB [auth N], FB [auth N], KA [auth F], LA [auth F], OB [auth R], PB [auth R], UA [auth J], VA [auth J], YB [auth V], ZB [auth V]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
OXY	BB [auth L], BC [auth V], DA [auth B], DB [auth M], DC [auth W], FA [auth C], FC [auth X], HA [auth D], HB [auth N], JA [auth E], JB [auth O], LB [auth P], NA [auth F], NB [auth Q], PA [auth G], RA [auth H], RB [auth R], TA [auth I], TB [auth S], VB [auth T], XA [auth J], XB [auth U], Z [auth A], ZA [auth K]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.271 
• R-Value Work: 0.243 
• R-Value Observed: 0.243 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 195.84	α = 90
b = 195.84	β = 90
c = 308.82	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-08 
Deposition Author(s): Flores, J.F., Fisher, C.R., Carney, S.L., Green, B.N., Freytag, J.K., Schaeffer, S.W., Royer, W.E.

Revision History  

• Version 1.0: 2005-02-08
  Type: Initial release
  
• Version 1.1: 2008-04-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2013-03-06
  Changes: Data collection