1RPQ | pdb_00001rpq

High Affinity IgE Receptor (alpha chain) Complexed with Tight-Binding E131 'zeta' Peptide from Phage Display

PDB DOI: https://doi.org/10.2210/pdb1RPQ/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2003-12-03 Released: 2004-07-20
Deposition Author(s): Stamos, J., Eigenbrot, C., Nakamura, G.R., Reynolds, M.E., Yin, J.P., Lowman, H.B., Fairbrother, W.J., Starovasnik, M.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.349 (Depositor), 0.341 (DCC)
R-Value Work:
0.294 (Depositor), 0.304 (DCC)
R-Value Observed:
0.294 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Convergent Recognition of the IgE Binding Site on the High-Affinity IgE Receptor.

Stamos, J., Eigenbrot, C., Nakamura, G.R., Reynolds, M.E., Yin, J.P., Lowman, H.B., Fairbrother, W.J., Starovasnik, M.A.

(2004) Structure 12: 1289-1301

PubMed: 15242605 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2004.04.015
Primary Citation Related Structures:
1RPQ

PubMed Abstract:
Two structurally distinct classes of peptides were recently identified by phage display that bind the high-affinity IgE receptor, FcepsilonRI, and block IgE binding and subsequent receptor activation. Both classes adopt highly stable structures in solution, one forming a beta hairpin, with the other forming a helical "zeta" structure. Despite these differences, the two classes bind competitively to the same site on the receptor. Structural analyses of both peptide-receptor complexes by NMR spectroscopy and/or X-ray crystallography reveal that the unrelated peptide scaffolds have nevertheless converged to present a similar three-dimensional surface to interact with FcepsilonRI and that their modes of interaction share a key feature of the IgE-FcepsilonRI complex, the proline/tryptophan sandwich.

Organizational Affiliation

Department of Protein Engineering, Genentech, Inc., One DNA Way, South San Francisco, CA 94080 USA. star@gene.com

Macromolecule Content

Total Structure Weight: 101.57 kDa
Atom Count: 6,757
Modeled Residue Count: 746
Deposited Residue Count: 788
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity immunoglobulin epsilon receptor alpha-subunit precursor	A, B, C, D	176	Homo sapiens	Mutation(s): 0 Gene Names: FCER1A, FCE1A
UniProt & NIH Common Fund Data Resources
Find proteins for P12319 (Homo sapiens) Explore P12319 Go to UniProtKB: P12319
PHAROS: P12319 GTEx: ENSG00000179639
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12319
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: P12319-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide E131	E [auth W], F [auth X], G [auth Y], H [auth Z]	21	N/A	Mutation(s): 0

Oligosaccharides

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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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth E], L [auth H]	3		N-Glycosylation	Interactions Focus chain I [auth E] Focus chain L [auth H] Interactions & Density Focus chain I [auth E] Focus chain L [auth H]
Glycosylation Resources
GlyTouCan: G47362BJ GlyCosmos: G47362BJ GlyGen: G47362BJ

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-4)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth F], M [auth I], P [auth L], S [auth O]	5		N-Glycosylation	Interactions Focus chain J [auth F] Focus chain M [auth I] Focus chain P [auth L] Focus chain S [auth O] Interactions & Density Focus chain J [auth F] Focus chain M [auth I] Focus chain P [auth L] Focus chain S [auth O]
Glycosylation Resources
GlyTouCan: G85872LH GlyCosmos: G85872LH GlyGen: G85872LH

Entity ID: 5
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	K [auth G], N [auth J], Q [auth M], T [auth P]	3		N-Glycosylation	Interactions Focus chain K [auth G] Focus chain N [auth J] Focus chain Q [auth M] Focus chain T [auth P] Interactions & Density Focus chain K [auth G] Focus chain N [auth J] Focus chain Q [auth M] Focus chain T [auth P]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O [auth K], R [auth N]	2		N-Glycosylation	Interactions Focus chain O [auth K] Focus chain R [auth N] Interactions & Density Focus chain O [auth K] Focus chain R [auth N]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain Z [auth D] SDF format, chain W [auth B] SDF format, chain U [auth A] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain W [auth B] MOL2 format, chain U [auth A] mmCIF format, chain X [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain W [auth B] mmCIF format, chain U [auth A]	U [auth A], W [auth B], X [auth C], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain U [auth A] Focus chain W [auth B] Focus chain X [auth C] Focus chain Z [auth D] Interactions & Density Focus chain U [auth A] Focus chain W [auth B] Focus chain X [auth C] Focus chain Z [auth D]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain AA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain AA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain AA [auth D]	AA [auth D], Y [auth C]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain Y [auth C] Interactions & Density Focus chain AA [auth D] Focus chain Y [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain BA [auth Z] SDF format, chain V [auth A] MOL2 format, chain BA [auth Z] MOL2 format, chain V [auth A] mmCIF format, chain BA [auth Z] mmCIF format, chain V [auth A]	BA [auth Z], V [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth Z] Focus chain V [auth A] Interactions & Density Focus chain BA [auth Z] Focus chain V [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017 Query on PRD_900017	I [auth E], L [auth H]	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor		Interactions Focus chain I [auth E] Focus chain L [auth H] Interactions & Density Focus chain I [auth E] Focus chain L [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.349 (Depositor), 0.341 (DCC)
R-Value Work: 0.294 (Depositor), 0.304 (DCC)
R-Value Observed: 0.294 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 199.7	α = 90
b = 149.7	β = 90
c = 104.1	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2004-07-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-07-20
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 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: 2023-08-23
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-09
Changes: Structure summary