9RN8 | pdb_00009rn8

Crystal structure of the photosensory core module (PCM) of a cyano-phenylalanine mutant oCNF205 of the bathy phytochrome Agp2 from Agrobacterium fabrum in the Pfr state.

PDB DOI: https://doi.org/10.2210/pdb9RN8/pdb

Classification: SIGNALING PROTEIN
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-06-19 Released: 2025-10-08
Deposition Author(s): Sauthof, L., Ebrahim, M., Scheerer, P.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.207 (Depositor), 0.214 (DCC)
R-Value Work:
0.178 (Depositor), 0.189 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Propagation of Photoinduced Electric Field Changes Through Phytochrome and their Impact on Conformational Transitions.

La Greca, M., Nguyen, A.D., Kraskov, A., Michael, N., Sauthof, L., Ebrahim, M., Katz, S., von Sass, J., Hoang, O.T., Budisa, N., Scheerer, P., Schlesinger, R., Mroginski, M.A., Hildebrandt, P.

(2025) Chemphyschem : e202500595-e202500595

PubMed: 40976591 Search on PubMed
DOI: https://doi.org/10.1002/cphc.202500595
Primary Citation of Related Structures:
9RN8

PubMed Abstract:
In phytochromes, photoisomerization of the chromophore and subsequent structural relaxations lead to the functionally essential secondary structure transition of the tongue, a phytochrome-specific protein segment. The coupling mechanism between chromophore and protein structural changes is yet not understood, but electric field changes are discussed to play an important role. In this work, electric field changes in the chromophore binding pocket (CBP) are confirmed to propagate over long distances through the protein and alter the electric field in the tongue region. An experimental-theoretical approach to analyze local electric fields using Stark reporters has been further developed. These are nitrile groups introduced site-specifically into the protein via noncanonical amino acids. The functional integrity of the variants is checked by crystallography and various spectroscopies. For the first time, functionally intact variants with substitutions in the tongue are generated. Based on frequency shifts and relative intensities of the nitrile stretching modes, hydrogen-bonding and noncovalent electric field contributions are separated. The field changes originating in the CBP are transduced to the tongue along a pathway via Phe192. Given a proper direction of the net electric field vector in the tongue region, the magnitude of the field may be sufficient to destabilize the tongue structure.

Organizational Affiliation

Experimental Physics: Genetic Biophysics, Freie Universität Berlin, Arnimallee 14, D-14195, Berlin, Germany.

Macromolecule Content

Total Structure Weight: 115.3 kDa
Atom Count: 8,818
Modeled Residue Count: 977
Deposited Residue Count: 1,014
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
histidine kinase	A	507	Agrobacterium fabrum str. C58	Mutation(s): 1 Gene Names: Atu2165 EC: 2.7.13.3
UniProt
Find proteins for A9CI81 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CI81 Go to UniProtKB: A9CI81
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9CI81
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
histidine kinase	B	507	Agrobacterium fabrum str. C58	Mutation(s): 1 Gene Names: Atu2165 EC: 2.7.13.3
UniProt
Find proteins for A9CI81 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CI81 Go to UniProtKB: A9CI81
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9CI81
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EL5 (Subject of Investigation/LOI) Query on EL5 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(E)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{(Z)-[(3E,4S)-3-ethylidene-4-methyl-5-oxopyrrolidin-2-ylidene]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic acid C₃₃ H₃₆ N₄ O₆ SNHIGJASYQUMKZ-IDFYGOSVSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	D [auth A], E [auth A], K [auth B], L [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B]	F [auth A], M [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLZ Query on MLZ	A	L-PEPTIDE LINKING	C₇ H₁₆ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.207 (Depositor), 0.214 (DCC)
R-Value Work: 0.178 (Depositor), 0.189 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.411	α = 90
b = 93.542	β = 90
c = 173.757	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

Sauthof, L.

Ebrahim, M.

Scheerer, P.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	CRC1078 - project number 221545957 - subproject B06
German Research Foundation (DFG)	Germany	EXC 311 2008/1 - UniSysCat - 390540038 - Research Unit E