8T7R | pdb_00008t7r

Crystal structure of human leukocyte antigen A*0101 in complex with the Fab of alloreactive antibody E07

• PDB DOI: https://doi.org/10.2210/pdb8T7R/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Cytomegalovirus
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-21 Released: 2024-12-25 
• Deposition Author(s): Green, T.J., Killian Jr, J.T., Qiu, S., Macon, K.J., Yang, G., King, R.G., Lund, F.E.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/Office of the Director, National Institutes of Health/National Center for Research Resources (NIH/NCRR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.84 Å
• R-Value Free: 
  0.263 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

B cell and antibody targeting of transplant alloantigen epitopes is supported by both self and allo-recognition

Killian Jr, J.T., King, R.G., Kizziah, J.L., Fucile, C.F., Diaz-Avalos, R., Qiu, S., Silva-Sanchez, A., Mousseau, B.J., Macon, K.J., Callahan, A.R., Yang, G., Hossain, E.M., Akther, J., Good, D.B., Kelso, S., Houp, J.A., Rosenblum, F., Porrett, P.M., Ong, S.C., Kumar, V., Ollmann Saphire, E., Kearney, J.F., Randall, T.D., Rosenberg, A.F., Green, T.J., Lund, F.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 50-mer - A12B12C9D8E6F3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 50-mer - A12B12C9D8E1F1G1H1I1J1K1L1M1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - E6 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A3B3 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 9-mer - A3B3F3 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 9-mer - A3B3E3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - D2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - D2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2E2 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 9-mer - A3B3E3 

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

Macromolecule Content 

• Total Structure Weight: 972.58 kDa 
• Atom Count: 63,611 
• Modeled Residue Count: 8,165 
• Deposited Residue Count: 8,787 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain from antibody JTK191b E07	A, EA [auth Y], F [auth E], JA [auth c], K [auth I], OA [auth g], P [auth M], SA [auth k], U [auth Q], UA [auth o], WA [auth s], Z [auth U]	214	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain from antibody JTK191b E07	AA [auth V], B, FA [auth Z], G [auth F], KA [auth d], L [auth J], PA [auth h], Q [auth N], TA [auth l], V [auth R], VA [auth p], XA [auth t]	240	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen (Fragment)	BA [auth W], C, GA [auth a], H [auth G], LA [auth e], M [auth K], QA [auth i], R [auth O], W [auth S]	274	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A
UniProt
Find proteins for F6IQR9 (Homo sapiens) Explore F6IQR9  Go to UniProtKB:  F6IQR9

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide	CA [auth 5], D [auth 0], HA [auth 6], I [auth 1], MA [auth 7], N [auth 2], RA [auth 8], S [auth 3], X [auth 4]	9	Cytomegalovirus	Mutation(s): 0
UniProt
Find proteins for P16790 (Human cytomegalovirus (strain AD169)) Explore P16790  Go to UniProtKB:  P16790

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	DA [auth X], E [auth D], IA [auth b], J [auth H], NA [auth f], O [auth L], T [auth P], Y [auth T]	99	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.84 Å
• R-Value Free:  0.263 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M38T7R

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 357.076	α = 90
b = 259.582	β = 133.13
c = 255.361	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-25 
Deposition Author(s): Green, T.J., Killian Jr, J.T., Qiu, S., Macon, K.J., Yang, G., King, R.G., Lund, F.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	T32AI007051
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19AI142737
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	T32DK007545
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P30CA013148
National Institutes of Health/Office of the Director	United States	S10OD027000
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	S10RR025528
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	S10RR028976

Revision History  

• Version 1.0: 2024-12-25
  Type: Initial release