7KRA

Cryo-EM structure of Saccharomyces cerevisiae ER membrane protein complex bound to Fab-DH4 in lipid nanodiscs

• PDB DOI: https://doi.org/10.2210/pdb7KRA/pdb
• EM Map EMD-23003: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN/IMMUNE SYSTEM
• Organism(s): Saccharomyces cerevisiae, Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2020-11-19 Released: 2020-12-02 
• Deposition Author(s): Miller-Vedam, L.E., Schirle Oakdale, N.S., Braeuning, B., Boydston, E.A., Sevillano, N., Popova, K.D., Bonnar, J.L., Shurtleff, M.J., Prabu, J.R., Stroud, R.M., Craik, C.S., Schulman, B.A., Weissman, J.S., Frost, A.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/Office of the Director

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A2B1C1D1E1F1G1H1I1J1K1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 311.51 kDa 
• Atom Count: 17,293 
• Modelled Residue Count: 2,164 
• Deposited Residue Count: 2,760 
• Unique protein chains: 11

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ER membrane protein complex subunit 1	A	760	Saccharomyces cerevisiae	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P25574 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25574  Go to UniProtKB:  P25574

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ER membrane protein complex subunit 2	B	292	Saccharomyces cerevisiae	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P47133 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P47133  Go to UniProtKB:  P47133

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ER membrane protein complex subunit 3	C	253	Saccharomyces cerevisiae	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P36039 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36039  Go to UniProtKB:  P36039

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ER membrane protein complex subunit 4	D	190	Saccharomyces cerevisiae	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P53073 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53073  Go to UniProtKB:  P53073

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ER membrane protein complex subunit 5	E	182	Saccharomyces cerevisiae	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P40540 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40540  Go to UniProtKB:  P40540

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
ER membrane protein complex subunit 6	F	108	Saccharomyces cerevisiae	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q12431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12431  Go to UniProtKB:  Q12431

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein SOP4	G	234	Saccharomyces cerevisiae	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P39543 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P39543  Go to UniProtKB:  P39543

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoplasmic reticulum membrane protein complex subunit 10	H	205	Saccharomyces cerevisiae	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q12025 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12025  Go to UniProtKB:  Q12025

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab DH4 heavy chain	I	254	Homo sapiens	Mutation(s): 0

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab DH4 light chain	J	234	Homo sapiens	Mutation(s): 0

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned helix	K [auth M], L [auth N]	24	Saccharomyces cerevisiae	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X3P	P [auth C]	[(2~{R})-1-octanoyloxy-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propan-2-yl] nonanoate C25 H51 N O8 P JUTWCUAFOQXGFE-HSZRJFAPSA-N
NAG	M [auth A], N [auth A], O [auth A], Q [auth G], R [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-02 
Deposition Author(s): Miller-Vedam, L.E., Schirle Oakdale, N.S., Braeuning, B., Boydston, E.A., Sevillano, N., Popova, K.D., Bonnar, J.L., Shurtleff, M.J., Prabu, J.R., Stroud, R.M., Craik, C.S., Schulman, B.A., Weissman, J.S., Frost, A.

---

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/Office of the Director	United States	1DP2OD017690-01

Revision History  

• Version 1.0: 2020-12-02
  Type: Initial release
  
• Version 1.1: 2020-12-09
  Changes: Database references