6M8P | pdb_00006m8p

Human ERAP1 bound to phosphinic pseudotripeptide inhibitor DG013

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 
    0.295 (Depositor), 0.298 (DCC) 
  • R-Value Work: 
    0.285 (Depositor), 0.286 (DCC) 
  • R-Value Observed: 
    0.286 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6M8P

Ligand Structure Quality Assessment 


This is version 2.3 of the entry. See complete history. 

Literature

Conformational dynamics linked to domain closure and substrate binding explain the ERAP1 allosteric regulation mechanism.

Maben, Z., Arya, R., Georgiadis, D., Stratikos, E., Stern, L.J.

(2021) Nat Commun 12: 5302-5302

  • DOI: https://doi.org/10.1038/s41467-021-25564-w
  • Primary Citation Related Structures: 
    6M8P, 6MGQ

  • PubMed Abstract: 

    The endoplasmic-reticulum aminopeptidase ERAP1 processes antigenic peptides for loading on MHC-I proteins and recognition by CD8 T cells as they survey the body for infection and malignancy. Crystal structures have revealed ERAP1 in either open or closed conformations, but whether these occur in solution and are involved in catalysis is not clear. Here, we assess ERAP1 conformational states in solution in the presence of substrates, allosteric activators, and inhibitors by small-angle X-ray scattering. We also characterize changes in protein conformation by X-ray crystallography, and we localize alternate C-terminal binding sites by chemical crosslinking. Structural and enzymatic data suggest that the structural reconfigurations of ERAP1 active site are physically linked to domain closure and are promoted by binding of long peptide substrates. These results clarify steps required for ERAP1 catalysis, demonstrate the importance of conformational dynamics within the catalytic cycle, and provide a mechanism for the observed allosteric regulation and Lys/Arg528 polymorphism disease association.

    • Organizational Affiliation: 
    • Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA.

Macromolecule Content 

  • Total Structure Weight: 2,338.35 kDa 
  • Atom Count: 155,927 
  • Modeled Residue Count: 18,942 
  • Deposited Residue Count: 19,778 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Endoplasmic reticulum aminopeptidase 1
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
899Homo sapiensMutation(s): 0 
Gene Names: ERAP1, APPILS, ARTS1, KIAA0525, UNQ584/PRO1154
EC: 3.4.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZ08 (Homo sapiens)
Explore Q9NZ08 
Go to UniProtKB:  Q9NZ08
PHAROS:  Q9NZ08
GTEx:  ENSG00000164307 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZ08
Glycosylation
Glycosylation Sites: 1
Go to GlyGen: Q9NZ08-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
AB [auth 0],
BA [auth b],
BB [auth 1],
CA [auth c],
AA [auth a],
AB [auth 0],
BA [auth b],
BB [auth 1],
CA [auth c],
CB [auth 2],
DA [auth d],
DB [auth 3],
EA [auth e],
EB [auth 4],
FA [auth f],
FB [auth 5],
GA [auth g],
GB [auth 6],
HA [auth h],
HB [auth 7],
IA [auth i],
IB [auth 8],
JA [auth j],
JB [auth 9],
KA [auth k],
KB [auth AA],
LA [auth l],
LB [auth BA],
MA [auth m],
MB [auth CA],
NA [auth n],
NB [auth DA],
OA [auth o],
PA [auth p],
QA [auth q],
RA [auth r],
SA [auth s],
TA [auth t],
UA [auth u],
VA [auth v],
W,
WA [auth w],
X,
XA [auth x],
Y,
YA [auth y],
Z,
ZA [auth z]
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P52

Query on P52


Download:Ideal Coordinates CCD File
CI [auth K]
CM [auth Q]
CO [auth T]
FC [auth B]
FE [auth E]
CI [auth K],
CM [auth Q],
CO [auth T],
FC [auth B],
FE [auth E],
FG [auth H],
FK [auth N],
KP [auth V],
LN [auth S],
MF [auth G],
MH [auth J],
ML [auth P],
NJ [auth M],
OD [auth D],
PB [auth A],
SM [auth R],
TO [auth U],
VK [auth O],
WC [auth C],
WE [auth F],
WG [auth I],
WI [auth L]
Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide
C27 H37 N4 O4 P
QKFOTLXPIIESQI-IEZKXTBUSA-N
NAG

Query on NAG


Download:Ideal Coordinates CCD File
AI [auth J]
AM [auth P]
BG [auth G]
CE [auth D]
CK [auth M]
AI [auth J],
AM [auth P],
BG [auth G],
CE [auth D],
CK [auth M],
DC [auth A],
HN [auth R],
IP [auth U],
KD [auth C],
KF [auth F],
KH [auth I],
KJ [auth L],
KL [auth O],
PM [auth Q],
QO [auth T],
RI [auth K],
TC [auth B],
TE [auth E],
TG [auth H],
TK [auth N],
YP [auth V],
ZN [auth S]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4

Query on SO4


Download:Ideal Coordinates CCD File
AC [auth A]
AD [auth C]
AE [auth D]
AF [auth F]
AG [auth G]
AC [auth A],
AD [auth C],
AE [auth D],
AF [auth F],
AG [auth G],
AH [auth I],
AJ [auth L],
AK [auth M],
AL [auth O],
AN [auth R],
AO [auth T],
AP [auth U],
BC [auth A],
BD [auth C],
BE [auth D],
BF [auth F],
BH [auth I],
BJ [auth L],
BK [auth M],
BL [auth O],
BN [auth R],
BP [auth U],
CC [auth A],
CD [auth C],
CF [auth F],
CG [auth G],
CH [auth I],
CJ [auth L],
CL [auth O],
CN [auth R],
CP [auth U],
DD [auth C],
DE [auth E],
DF [auth F],
DG [auth H],
DH [auth I],
DI [auth K],
DJ [auth L],
DK [auth N],
DL [auth O],
DM [auth Q],
DN [auth R],
DO [auth T],
DP [auth U],
ED [auth C],
EF [auth F],
EH [auth I],
EI [auth K],
EJ [auth L],
EL [auth O],
EM [auth Q],
EN [auth R],
EO [auth T],
EP [auth U],
FD [auth C],
FF [auth F],
FH [auth I],
FI [auth K],
FJ [auth L],
FL [auth O],
FM [auth Q],
FN [auth R],
FO [auth T],
FP [auth U],
GC [auth B],
GD [auth C],
GE [auth E],
GF [auth F],
GG [auth H],
GH [auth I],
GI [auth K],
GJ [auth L],
GK [auth N],
GL [auth O],
GM [auth Q],
GN [auth R],
GO [auth T],
GP [auth U],
HC [auth B],
HD [auth C],
HE [auth E],
HF [auth F],
HG [auth H],
HH [auth I],
HI [auth K],
HJ [auth L],
HK [auth N],
HL [auth O],
HM [auth Q],
HO [auth T],
HP [auth U],
IC [auth B],
ID [auth C],
IE [auth E],
IF [auth F],
IG [auth H],
IH [auth I],
II [auth K],
IJ [auth L],
IK [auth N],
IL [auth O],
IM [auth Q],
IN [auth R],
IO [auth T],
JC [auth B],
JD [auth C],
JE [auth E],
JF [auth F],
JG [auth H],
JH [auth I],
JI [auth K],
JJ [auth L],
JK [auth N],
JL [auth O],
JM [auth Q],
JN [auth S],
JO [auth T],
KC [auth B],
KE [auth E],
KG [auth H],
KI [auth K],
KK [auth N],
KM [auth Q],
KO [auth T],
LC [auth B],
LD [auth C],
LE [auth E],
LG [auth H],
LI [auth K],
LJ [auth M],
LK [auth N],
LM [auth Q],
LO [auth T],
LP [auth V],
MC [auth B],
MD [auth D],
ME [auth E],
MG [auth H],
MI [auth K],
MK [auth N],
MM [auth Q],
MN [auth S],
MO [auth T],
MP [auth V],
NC [auth B],
NE [auth E],
NF [auth G],
NG [auth H],
NH [auth J],
NI [auth K],
NK [auth N],
NL [auth P],
NM [auth Q],
NN [auth S],
NO [auth T],
NP [auth V],
OC [auth B],
OE [auth E],
OF [auth G],
OG [auth H],
OH [auth J],
OI [auth K],
OJ [auth M],
OK [auth N],
OL [auth P],
OM [auth Q],
ON [auth S],
OO [auth T],
OP [auth V],
PC [auth B],
PD [auth D],
PE [auth E],
PF [auth G],
PG [auth H],
PH [auth J],
PI [auth K],
PJ [auth M],
PK [auth N],
PL [auth P],
PN [auth S],
PO [auth T],
PP [auth V],
QB [auth A],
QC [auth B],
QD [auth D],
QE [auth E],
QF [auth G],
QG [auth H],
QH [auth J],
QI [auth K],
QJ [auth M],
QK [auth N],
QL [auth P],
QM [auth Q],
QN [auth S],
QP [auth V],
RB [auth A],
RC [auth B],
RD [auth D],
RE [auth E],
RF [auth G],
RG [auth H],
RH [auth J],
RJ [auth M],
RK [auth N],
RL [auth P],
RN [auth S],
RO [auth U],
RP [auth V],
SB [auth A],
SC [auth B],
SD [auth D],
SE [auth E],
SF [auth G],
SG [auth H],
SH [auth J],
SI [auth K],
SJ [auth M],
SK [auth N],
SL [auth P],
SN [auth S],
SP [auth V],
TB [auth A],
TD [auth D],
TF [auth G],
TH [auth J],
TI [auth K],
TJ [auth M],
TL [auth P],
TM [auth R],
TN [auth S],
TP [auth V],
UB [auth A],
UC [auth B],
UD [auth D],
UE [auth F],
UF [auth G],
UG [auth I],
UH [auth J],
UI [auth L],
UJ [auth M],
UL [auth P],
UM [auth R],
UN [auth S],
UO [auth U],
UP [auth V],
VB [auth A],
VD [auth D],
VF [auth G],
VH [auth J],
VJ [auth M],
VL [auth P],
VM [auth R],
VN [auth S],
VO [auth U],
VP [auth V],
WB [auth A],
WD [auth D],
WF [auth G],
WH [auth J],
WJ [auth M],
WK [auth O],
WL [auth P],
WM [auth R],
WN [auth S],
WO [auth U],
WP [auth V],
XB [auth A],
XC [auth C],
XD [auth D],
XE [auth F],
XF [auth G],
XG [auth I],
XH [auth J],
XI [auth L],
XJ [auth M],
XK [auth O],
XL [auth P],
XM [auth R],
XN [auth S],
XO [auth U],
XP [auth V],
YB [auth A],
YC [auth C],
YD [auth D],
YE [auth F],
YF [auth G],
YG [auth I],
YH [auth J],
YI [auth L],
YJ [auth M],
YK [auth O],
YL [auth P],
YM [auth R],
YN [auth S],
YO [auth U],
ZB [auth A],
ZC [auth C],
ZD [auth D],
ZE [auth F],
ZF [auth G],
ZG [auth I],
ZH [auth J],
ZI [auth L],
ZJ [auth M],
ZK [auth O],
ZL [auth P],
ZM [auth R],
ZO [auth U]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN

Query on ZN


Download:Ideal Coordinates CCD File
BI [auth K]
BM [auth Q]
BO [auth T]
EC [auth B]
EE [auth E]
BI [auth K],
BM [auth Q],
BO [auth T],
EC [auth B],
EE [auth E],
EG [auth H],
EK [auth N],
JP [auth V],
KN [auth S],
LF [auth G],
LH [auth J],
LL [auth P],
MJ [auth M],
ND [auth D],
OB [auth A],
RM [auth R],
SO [auth U],
UK [auth O],
VC [auth C],
VE [auth F],
VG [auth I],
VI [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
P52 BindingDB:  6M8P IC50: min: 33, max: 4.30e+4 (nM) from 6 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free:  0.295 (Depositor), 0.298 (DCC) 
  • R-Value Work:  0.285 (Depositor), 0.286 (DCC) 
  • R-Value Observed: 0.286 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.79α = 90
b = 548.684β = 90
c = 589.056γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01AI038996

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2022-06-01
    Changes: Database references, Structure summary
  • Version 2.2: 2023-10-11
    Changes: Data collection, Refinement description
  • Version 2.3: 2024-11-13
    Changes: Structure summary