5MZA

The DBLb domain of PF11_0521 PfEMP1 bound to human ICAM-1

• PDB DOI: https://doi.org/10.2210/pdb5MZA/pdb

• Classification: CELL ADHESION
• Organism(s): Plasmodium falciparum 3D7, Homo sapiens
• Expression System: Escherichia coli, Homo sapiens
• Mutation(s): No 


• Deposited: 2017-01-31 Released: 2017-03-22 
• Deposition Author(s): Lennartz, F., Higgins, M.K.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 0.236 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 

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: 77.8 kDa 
• Atom Count: 5,086 
• Modelled Residue Count: 626 
• Deposited Residue Count: 674 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Erythrocyte membrane protein 1 (PfEMP1)	A	488	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PF11_0521, PF3D7_1150400
UniProt
Find proteins for Q8IHM0 (Plasmodium falciparum (isolate 3D7)) Explore Q8IHM0  Go to UniProtKB:  Q8IHM0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Intercellular adhesion molecule 1	B	186	Homo sapiens	Mutation(s): 0  Gene Names: ICAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P05362 (Homo sapiens) Explore P05362  Go to UniProtKB:  P05362
PHAROS:  P05362 GTEx:  ENSG00000090339

Oligosaccharides

Help

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP	G [auth B]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N
3PO	D [auth A]	TRIPHOSPHATE H5 O10 P3 UNXRWKVEANCORM-UHFFFAOYSA-N
NAG	E [auth B], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 0.236 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.639	α = 90
b = 109.83	β = 90
c = 112.83	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-03-22 
Deposition Author(s): Lennartz, F., Higgins, M.K.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	101020/Z/13/Z

Revision History  

• Version 1.0: 2017-03-22
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2020-10-07
  Changes: Structure summary