9P4E | pdb_00009p4e

Crystal Structure of Engineered glutamine binding protein and a Gd-DOTA ligand - no GLN bound

• PDB DOI: https://doi.org/10.2210/pdb9P4E/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-06-16 Released: 2026-01-14 
• Deposition Author(s): Bruchs, A.T., Wilson, C.A., Boggs, D.G., Fatima, S., Bridwell-Rabb, J., Olshansky, L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.226 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Development of a glutamine-responsive MRI contrast agent.

Wilson, C.A., Bruchs, A.T., Fatima, S., Boggs, D.G., Bridwell-Rabb, J., Olshansky, L.

(2026) Chem Sci 17: 2781-2790

• PubMed: 41395538 
• DOI: https://doi.org/10.1039/d5sc05987a
• Primary Citation Related Structures: 
  9P4D, 9P4E


• PubMed Abstract: 
  

  Magnetic resonance imaging (MRI) is widely used to visualize disease, and image quality can be improved through use of MRI contrast agents. Currently available agents produce a signal based solely on spatial distribution, but modern metabolic profiling has uncovered a variety of biomarkers for disease. For example, tumors greatly increase their uptake and catabolism of glutamine (Gln), leading to modified local concentration. Our laboratory previously developed a switchable artificial metalloprotein (swArM) platform in which Gln-binding causes a protein conformational change that modifies the physicochemical environment of an installed metallocofactor. Installing MRI-active metallocofactors within swArMs, we present a proof-of-concept approch toward the development of an analyte-responsive MRI contrast agent. To develop these swArMs, we tested several MRI-active metals (Gd ³⁺ , Dy ³⁺ ), chelating ligands (DOTA, DTPA, NOTA), and attachment sites, as well as the impacts of peripheral mutations on the Gln-responsive signal. In each case, metal content was analytically defined, and Gln-binding affinity was determined by isothermal titration calorimetry. Circular dichroism was used to verify that our swArMs could still undergo the conformational change. X-ray diffraction structures of the apo- and holo- swArMs further revealed that the metallocofactor is significantly solvent-exposed in both conformations, but exhibits additional interactions with the protein in the holo- state coinciding with the observed increase in T ₂ relaxivity of ∼60% upon Gln-binding.

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Organizational Affiliation: 
• Department of Chemistry, University of Illinois Urbana-Champaign 600 S. Mathews Ave Urbana IL 61801 USA.
Department of Chemistry, University of Michigan, 930 N. University Ave Ann Arbor MI 48109 USA.
Center for Biophysics and Quantitative Biology, Chemical and Biomolecular Engineering, Materials Research Laboratory, and the Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign 600 S. Mathews Ave Urbana IL 61801 USA [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 26.92 kDa 
• Atom Count: 2,219 
• Modeled Residue Count: 224 
• Deposited Residue Count: 229 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino acid ABC transporter substrate-binding protein	A [auth C]	229	Escherichia coli	Mutation(s): 2  Gene Names:  glnH, A5U30_004091, A6592_04880, A8499_000176, A9X72_16950, AAG43_003583, ACN68_16860, ACN81_02400, ACU57_05845, AF998_000125, AM464_21485, APX88_17575, AT335_000554, AT845_002764, AW118_24500, AW119_03915, AWP47_29145, B6R12_003536, B6R15_002883, B6R31_003222, B6R48_003973, B6R87_003886, BANRA_01322, BANRA_01764, BEA19_14205, BER14_07540, BF481_003043, BG944_004267, BGM66_000966, BHS81_04935, BJI68_11495, BJJ90_17825, BK292_21345, BK383_19105, BLM69_000575, BMC79_000611, BMT49_05685, BMT50_00560, BMT91_20520, BN17_06101, BO068_000746, BOH76_16995, BON63_24725, BON64_24190, BON65_04740, BON66_07455, BON67_25290, BON68_02720, BON69_08400, BON70_24775, BON71_14305, BON72_22420, BON73_01195, BON74_14830, BON75_15470, BON76_25420, BON77_09375, BON78_20655, BON79_20060, BON80_12630, BON81_19085, BON82_15305, BON83_05500, BON84_13940, BON86_21740, BON87_16800, BON88_07465, BON89_22820, BON90_14295, BON91_21900, BON92_22285, BON93_04225, BON94_25770, BON95_05775, BON96_27115, BON97_10525, BON98_19710, BR158_002878, BRV02_000648, BSR05_11095, BTB68_001717, BTQ06_26205, BUO55_004168, BvCmsF30A_02312, BvCmsHHP019_04964, BvCmsKKP061_03133, BvCmsKSNP073_02686, BVL39_24445, BXT93_09325, BZL69_00955, C0P57_004641, C1Q91_004053, C2121_002453, C2M16_01565, C2R31_002978, C2U48_05980, C3F40_08525, C5N07_02720, C5Y87_11455, C9114_21285, C9160_24490, C9E67_21255, C9Z68_13890, CA593_25060, CCS08_19690, CCV12_002704, CDC27_03365, CDL36_05995, CDL37_06170, CF22_003152, CG831_000699, CHM61_001352, CIG67_24135, CO706_26845, CQ986_002219, CR538_17365, CR539_08495, CR628_003110, CTR35_001347, CV83915_00768, CWS33_06680, CX938_000617, CXJ73_000498, CY655_04230, D0X26_05085, D1912_20655, D1H34_001169, D3822_09995, D3C88_05045, D3G36_03255, D3Y67_17015, D4N09_12520, D4U49_00030, D9D43_04855, D9D77_09815, D9E34_09280, D9E49_16110, D9H94_11690, D9J03_11000, D9J61_05355, DAH17_03825, DAH18_19240, DAH19_07490, DAH20_21020, DAH21_16625, DAH22_20195, DAH23_12545, DAH24_12625, DAH25_13880, DAH26_12570, DAH27_27195, DAH28_26570, DAH29_21215, DAH30_24830, DAH31_23660, DAH32_25755, DAH33_16740, DAH34_00565, DAH35_19590, DAH36_01785, DAH37_00035, DAH38_23920, DAH40_16855, DAH41_26115, DAH42_14420, DAH43_13740, DAH45_14115, DAH46_16030, DAH47_10645, DAH48_08930, DAH49_15255, DAH50_02775, DD762_19985, DEN86_16580, DEN87_25365, DEN88_18460, DEN89_18240, DEN90_15895, DEN91_18520, DEN92_25370, DEN93_25685, DEN94_25170, DEN95_25645, DEN96_14460, DEN97_05945, DEN98_14610, DEN99_03305, DEO00_15605, DEO01_16930, DEO02_15845, DEO03_02745, DEO04_17445, DEO05_17315, DEO06_16065, DEO07_16850, DEO08_10875, DEO09_17170, DEO10_17430, DEO11_17320, DEO12_17235, DEO13_25310, DEO14_25015, DEO15_18570, DEO17_18420, DEO18_14095, DEO19_25855, DEO20_09480, DIV22_24420, DKP82_24310, DM870_16080, DN627_03140, DNX30_21735, DRW19_18320, DS732_09030, DTL43_10730, DTL90_03445, DTM45_05760, DU321_00670, DXT69_17235, DXT70_03865, DXT71_08710, DXT73_10050, E0I42_20880, E2112_02675, E2113_01945, E2114_18730, E2115_17055, E2116_04330, E2117_24095, E2118_16300, E2119_12420, E2120_04215, E2121_18185, E2122_15175, E2123_15570, E2124_10840, E2125_18565, E2127_00470, E2128_04955, E2129_10405, E2130_05520, E2131_16230, E2132_01450, E2133_04840, E2134_04965, E2135_16085, E2136_14980, E2646_20010, E3O05_01530, E4K51_02810, E4T14_00550, E4T84_17465, E5H86_25390, E5M02_22525, E5P22_03440, E5P23_09650, E5P24_07820, E5P25_14380, E5P26_02375, E5P27_03730, E5P28_05135, E5P29_02255, E5P30_11875, E5P31_05030, E5P32_00405, E5P33_13470, E5P34_03095, E5P35_02485, E5P36_15665, E5P37_20315, E5P39_19970, E5P40_02695, E5P41_16665, E5P42_12050, E5P43_17005, E5P44_18530, E5P45_22380, E5P46_16045, E5P47_19935, E5P48_15405, E5P49_19430, E5P50_22740, E5P51_16920, E5S34_18760, E5S35_18835, E5S36_04930, E5S37_23235, E5S38_16415, E5S39_18510, E5S43_19010, E5S44_19440, E5S45_23380, E5S46_22040, E5S47_18610, E5S48_18775, E5S51_14615, E5S52_10650, E5S53_16880, E5S54_25355, E5S55_16870, E5S56_20090, E5S57_09335, E5S58_12745, E5S61_14780, E5S62_04320, E6C80_01100, E6D34_16620, EA239_02055, EA435_03075, EAI46_17535, EAN77_08520, EAX79_16230, EC1094V2_3069, EC95NR1_05084, ECs0889, ED648_06680, EHD79_17160, EI021_00555, EIA08_01310, EIZ93_04910, EKI52_06410, EL79_3071, EL80_3032, ELT16_02415, ELT17_17330, ELT20_02820, ELT21_01480, ELT22_07560, ELT23_02015, ELT24_02785, ELT25_04925, ELT26_09185, ELT27_07495, ELT28_15430, ELT29_09190, ELT30_04155, ELT31_02235, ELT32_01320, ELT33_01125, ELT34_02155, ELT35_01150, ELT36_07860, ELT38_02015, ELT39_12720, ELT40_06625, ELT41_10995, ELT44_00485, ELT45_07655, ELT46_05645, ELT48_02765, ELT49_11575, ELT50_00370, ELT51_04720, ELT52_01735, ELT54_03790, ELT55_02630, ELT56_04370, ELT58_13405, ELT59_01975, ELT60_02685, ELT61_00525, ELT63_00400, ELT72_09395, ELU07_01290, ELU82_01275, ELU83_00030, ELU85_01090, ELU88_02755, ELU89_06090, ELU90_16660, ELU91_09660, ELU94_20245, ELU95_04135, ELU96_01710, ELU97_02075, ELU98_07325, ELU99_17975, ELV00_00990, ELV01_02685, ELV02_04500, ELV03_02685, ELV04_09130, ELV05_01070, ELV07_02685, ELV08_05490, ELV09_09705, ELV10_03635, ELV11_00495, ELV12_17700, ELV13_05135, ELV15_08005, ELV16_06920, ELV20_01690, ELV21_07280, ELV22_03390, ELV23_04940, ELV26_19830, ELV28_13395, ELV29_14030, ELV40_13070, ELX48_20960, ELX61_08885, ELX66_13645, ELX68_03535, ELX69_04805, ELX76_06605, ELX79_08650, ELX85_04825, ELX96_24945, ELY02_21695, ELY32_15660, ELY36_07870, ELY39_10000, ELY41_22740, ELY48_10875, EN85_004581, ERS085406_04011, ERS139208_02685, EWK56_11475, ExPECSC038_02876, EXX13_17615, EYV17_11920, EYV18_03835, F0L67_04275, F2N20_02135, F2N31_03410, F3N40_12265, F7F11_11485, F7N46_08470, F9413_07780, F9461_01305, F9B07_02710, F9S83_08475, F9V24_04485, F9X20_12650, FDM60_08540, FE584_14605, FE587_14715, FEJ01_13600, FFF58_04660, FGG80_18845, FHO90_02740, FHQ91_05095, FIJ20_11900, FJQ40_17745, FJQ51_03360, FJQ53_08590, FKO60_07285, FOI11_009340, FOI11_10705, FPI65_04950, FPJ29_13820, FPS11_01585, FQF29_02765, FV293_02200, FVB16_07150, FWK02_14955, FY127_05225, FZC17_24290, FZN31_16475, FZU14_07000, G3813_001838, G3V95_03410, G3W53_12740, G4A38_09725, G4A47_02555, G5603_02180, G7630_000206, G9448_06715, GAI66_11760, GAI89_13630, GAJ12_17235, GAJ26_02185, GF147_05165, GF699_09700, GFY34_01840, GIB53_03185, GJ11_04510, GJO56_05855, GKF66_09425, GKF89_13835, GNW61_02415, GNZ05_09120, GOP25_10140, GP711_00870, GP944_02795, GP965_17210, GP979_15650, GQM04_08380, GQM13_17840, GQM21_08920, GQN34_06325, GQW07_06480, GQW68_09320, GQW80_16390, GRC73_03245, GRO95_00200, GRW05_01550, GRW24_15895, GRW56_11730, GRW57_13110, GSM54_17415, GSY44_21500, GTP88_11170, GUC01_03260, GUI33_12255, H0O37_11575, H0O39_10830, H0O72_02630, HEP30_007075, HEP34_000682, HHH44_004674, HI055_001651, HIE29_000308, HIN64_003897, HJQ60_003183, HJU54_001291, HKA49_004171, HL563_07185, HL601_10425, HLV18_05320, HLX92_21635, HLZ50_00225, HmCms169_02183, HMJ82_04430, HMV95_02550, HMW38_01730, HNC36_00575, HNC59_02155, HNC66_13445, HNC99_06490, HND12_01310, HV109_16015, HV209_04855, HVV39_21020, HVW04_06960, HVW19_18030, HVW43_08305, HVY77_17775, HVZ71_16640, HX136_17495, I6H00_09980, I6H01_21610, I6H02_22350, IA00_002027, IFB95_003951, IH768_00950, IH772_11995, IT029_003785, J0541_000988, J4S20_005071, J5U05_002124, JE86ST02C_09210, JE86ST05C_09750, JFD_02409, JNP96_08670, NCTC10082_05067, NCTC10089_03418, NCTC10090_00382, NCTC10418_05048, NCTC10429_05756, NCTC10865_04252, NCTC11181_00607, NCTC12950_03687, NCTC13127_04610, NCTC13216_03355, NCTC4450_03842, NCTC7922_06781, NCTC7927_03810, NCTC7928_05513, NCTC8008_02951, NCTC8009_06196, NCTC8179_02263, NCTC8333_03962, NCTC8450_01827, NCTC8500_03700, NCTC8621_03555, NCTC8959_00379, NCTC8960_00488, NCTC9001_01370, NCTC9036_03440, NCTC9037_03540, NCTC9075_04560, NCTC9111_03455, NCTC9702_03882, NCTC9706_00702, NCTC9775_01675, NCTC9777_03409, NCTC9962_02368, ND22_002874, RG28_00455, SAMEA3472044_00248, SAMEA3472056_00231, SAMEA3472147_02754, SAMEA3751407_00314, SAMEA3752557_02233, SAMEA3753106_00906, TUM18780_29030, WP4S18E07_30170, WR15_25350, XU56_002013
UniProt
Find proteins for P0AEQ3 (Escherichia coli (strain K12)) Explore P0AEQ3  Go to UniProtKB:  P0AEQ3

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1C21 (Subject of Investigation/LOI)	H [auth C]	4-oxo-4-[(2-{2-[4,7,10-tris(carboxymethyl)-1,4,7,10-tetraazacyclododecan-1-yl]acetamido}ethyl)amino]butanoic acid C22 H38 N6 O10 PAUKHVCHLHGUBL-UHFFFAOYSA-N
GD3 (Subject of Investigation/LOI)	P [auth C]	GADOLINIUM ION Gd RJOJUSXNYCILHH-UHFFFAOYSA-N
SO4	B [auth C], C, N [auth C], O [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	I [auth C], J [auth C], K [auth C], L [auth C], M [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	D [auth C], F [auth C], G [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.226 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.161	α = 90
b = 128.161	β = 90
c = 119.828	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-01-14 
Deposition Author(s): Bruchs, A.T., Wilson, C.A., Boggs, D.G., Fatima, S., Bridwell-Rabb, J., Olshansky, L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM138138

Revision History  

• Version 1.0: 2026-01-14
  Type: Initial release
  
• Version 1.1: 2026-02-11
  Changes: Database references