1PC8 | pdb_00001pc8

Crystal Structure of a novel form of mistletoe lectin from Himalayan Viscum album L. at 3.8A resolution

• PDB DOI: https://doi.org/10.2210/pdb1PC8/pdb

• Classification: HYDROLASE
• Organism(s): Viscum album
• Mutation(s): No 


• Deposited: 2003-05-16 Released: 2004-06-22 
• Deposition Author(s): Mishra, V., Ethayathulla, A.S., Paramasivam, M., Singh, G., Yadav, S., Kaur, P., Sharma, R.S., Babu, C.R., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 
  0.271 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Structure of a novel ribosome-inactivating protein from a hemi-parasitic plant inhabiting the northwestern Himalayas.

Mishra, V., Ethayathulla, A.S., Sharma, R.S., Yadav, S., Krauspenhaar, R., Betzel, C., Babu, C.R., Singh, T.P.

(2004) Acta Crystallogr D Biol Crystallogr 60: 2295-2304

• PubMed: 15583377 
• DOI: https://doi.org/10.1107/S0907444904023534
• Primary Citation Related Structures: 
  1PC8


• PubMed Abstract: 
  

  This is the first report of the structural studies of a novel ribosome-inactivating protein (RIP) obtained from the Himalayan mistletoe (Viscum album) (HmRip). HmRip is a type II heterodimeric protein consisting of a toxic enzyme (A-chain) with an active site for ribosome inactivation and a lectin subunit (B-chain) with well defined sugar-binding sites. The crystal structure of HmRip has been determined at 3.8 A resolution and refined to a crystallographic R factor of 0.228 (R(free) = 0.271). A comparison of this structure with other type II RIPs reveals the presence of distinct structural features in the active site of the A-chain and in the 2gamma sugar-binding site of the B-chain. The conformation of the side chain of Tyr110, which is a conserved active-site residue in the A subunit, is strikingly different from those observed in other mistletoe RIPs, indicating its unique substrate-binding preference. The deletion of two important residues from the kink region after Ala231 in the 2gamma subdomain of the B-chain results in a significantly different conformation of the sugar-binding pocket. A ribosome-recognition site has also been identified in HmRip. The site is a shallow cavity, with the conserved residues Arg51, Asp70, Thr72 and Asn73 involved in the binding. The conformations of the antigenic epitopes of residues 1-20, 85-103 and 206-223 differ from those observed in other type II RIPs, resulting in the distinct antigenicity and pharmacological properties of HmRip.

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Organizational Affiliation: 
• Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 55.86 kDa 
• Atom Count: 3,935 
• Modeled Residue Count: 495 
• Deposited Residue Count: 495 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Himalayan mistletoe ribosome-inactivating protein	A	240	Viscum album	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for Q6ITZ3 (Viscum album) Explore Q6ITZ3  Go to UniProtKB:  Q6ITZ3
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Himalayan mistletoe ribosome-inactivating protein	B	255	Viscum album	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for Q6ITZ3 (Viscum album) Explore Q6ITZ3  Go to UniProtKB:  Q6ITZ3
Glycosylation
Glycosylation Sites: 3

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free:  0.271 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.182	α = 90
b = 109.182	β = 90
c = 309.44	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-22 
Deposition Author(s): Mishra, V., Ethayathulla, A.S., Paramasivam, M., Singh, G., Yadav, S., Kaur, P., Sharma, R.S., Babu, C.R., Singh, T.P.

Revision History  

• Version 1.0: 2004-06-22
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-10-25
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-30
  Changes: Structure summary