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- PDB-3n95: Crystal structure of human CRFR2 alpha extracellular domain in co... -

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Basic information

Entry
Database: PDB / ID: 3n95
TitleCrystal structure of human CRFR2 alpha extracellular domain in complex with Urocortin 2
Components
  • Maltose binding protein-CRFR2 alpha extracellular domain
  • Urocortin-2
KeywordsMembrane protein / Hormone / Class B-GPCR / Extracellular domain / CRFR2 alpha extracellular domain / Neuropeptide / Selectivity
Function / homology
Function and homology information


corticotropin-releasing hormone receptor binding / corticotropin-releasing hormone receptor 2 binding / Class B/2 (Secretin family receptors) / detection of maltose stimulus / maltose transport complex / carbohydrate transport / hormone binding / carbohydrate transmembrane transporter activity / maltose binding / maltose transport ...corticotropin-releasing hormone receptor binding / corticotropin-releasing hormone receptor 2 binding / Class B/2 (Secretin family receptors) / detection of maltose stimulus / maltose transport complex / carbohydrate transport / hormone binding / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / cellular response to nutrient levels / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / digestion / hormone-mediated signaling pathway / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / hormone activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / extracellular space / extracellular region / membrane
Similarity search - Function
Urocortin II/III / Corticotropin-releasing factor / Corticotropin-releasing factor family / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / Hormone receptor domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein ...Urocortin II/III / Corticotropin-releasing factor / Corticotropin-releasing factor family / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / Hormone receptor domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Urocortin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsPal, K. / Swaminathan, K. / Pioszak, A.A. / Xu, H.E.
CitationJournal: To be Published
Title: Structural basis of ligand selectivity in human CRFR1 and CRFR2 alpha extracellular domain
Authors: Pal, K. / Swaminathan, K. / Pioszak, A.A. / Xu, H.E.
History
DepositionMay 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose binding protein-CRFR2 alpha extracellular domain
B: Maltose binding protein-CRFR2 alpha extracellular domain
C: Maltose binding protein-CRFR2 alpha extracellular domain
D: Maltose binding protein-CRFR2 alpha extracellular domain
E: Urocortin-2
F: Urocortin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,44010
Polymers216,0716
Non-polymers1,3694
Water4,900272
1
A: Maltose binding protein-CRFR2 alpha extracellular domain
C: Maltose binding protein-CRFR2 alpha extracellular domain
E: Urocortin-2
hetero molecules

B: Maltose binding protein-CRFR2 alpha extracellular domain
D: Maltose binding protein-CRFR2 alpha extracellular domain
F: Urocortin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,44010
Polymers216,0716
Non-polymers1,3694
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area15580 Å2
ΔGint-73 kcal/mol
Surface area79280 Å2
MethodPISA
2
A: Maltose binding protein-CRFR2 alpha extracellular domain
C: Maltose binding protein-CRFR2 alpha extracellular domain
E: Urocortin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,7205
Polymers108,0353
Non-polymers6852
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-18 kcal/mol
Surface area41530 Å2
MethodPISA
3
B: Maltose binding protein-CRFR2 alpha extracellular domain
D: Maltose binding protein-CRFR2 alpha extracellular domain
F: Urocortin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,7205
Polymers108,0353
Non-polymers6852
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-18 kcal/mol
Surface area41730 Å2
MethodPISA
4
A: Maltose binding protein-CRFR2 alpha extracellular domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4892
Polymers53,1471
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: Maltose binding protein-CRFR2 alpha extracellular domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4892
Polymers53,1471
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
C: Maltose binding protein-CRFR2 alpha extracellular domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4892
Polymers53,1471
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
D: Maltose binding protein-CRFR2 alpha extracellular domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4892
Polymers53,1471
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
E: Urocortin-2


Theoretical massNumber of molelcules
Total (without water)1,7421
Polymers1,7421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
F: Urocortin-2


  • defined by author
  • 1.74 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,7421
Polymers1,7421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.311, 212.068, 107.319
Angle α, β, γ (deg.)90.000, 104.540, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12B
22C
13C
23D
14A
24B
15B
25C
16C
26D
17A
27B
18B
28C
19C
29D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSALAALA1AA-369 - -63 - 366
21LYSLYSALAALA1BB-369 - -63 - 366
12LYSLYSALAALA1BB-369 - -63 - 366
22LYSLYSALAALA1CC-369 - -63 - 366
13LYSLYSALAALA1CC-369 - -63 - 366
23LYSLYSALAALA1DD-369 - -63 - 366
14ALAALAGLYGLY2AA4 - 26376 - 398
24ALAALAGLYGLY2BB4 - 26376 - 398
15ALAALAGLYGLY2BB4 - 26376 - 398
25ALAALAGLYGLY2CC4 - 26376 - 398
16ALAALAGLYGLY2CC4 - 26376 - 398
26ALAALAGLYGLY2DD4 - 26376 - 398
17SERSERGLUGLU2AA38 - 99410 - 471
27SERSERGLUGLU2BB38 - 99410 - 471
18SERSERGLUGLU2BB38 - 99410 - 471
28SERSERGLUGLU2CC38 - 99410 - 471
19SERSERGLUGLU2CC38 - 99410 - 471
29SERSERGLUGLU2DD38 - 99410 - 471

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

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Components

#1: Protein
Maltose binding protein-CRFR2 alpha extracellular domain


Mass: 53146.746 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Human CRFR2 alpha / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9*PLUS
#2: Protein/peptide Urocortin-2 / Urocortin II / Ucn II / Stresscopin-related peptide / Urocortin-related peptide


Mass: 1741.993 Da / Num. of mol.: 2 / Fragment: UNP residues 94-109 / Source method: obtained synthetically / Details: Human Urocortin 2 / References: UniProt: Q96RP3
#3: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% PEG 6000 0.1M ADA (pH 6.0) 0.1M MgCl2 12% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.72→50 Å / Num. obs: 62181 / % possible obs: 98.93 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.15 / Net I/σ(I): 14.28
Reflection shellResolution: 2.72→2.82 Å / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.82

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N93

3n93


Resolution: 2.72→50 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.89 / Occupancy max: 1 / Occupancy min: 1 / SU B: 30.68 / SU ML: 0.287 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.266 3148 5.1 %RANDOM
Rwork0.224 ---
obs0.226 62071 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 220 Å2 / Biso mean: 24.744 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å2-0.07 Å2
2--1.49 Å20 Å2
3----2.6 Å2
Refinement stepCycle: LAST / Resolution: 2.72→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14722 0 92 272 15086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02215186
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9720659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.27251891
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61725.618671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93152471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0381542
X-RAY DIFFRACTIONr_chiral_restr0.0840.22269
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111554
X-RAY DIFFRACTIONr_mcbond_it0.2171.59457
X-RAY DIFFRACTIONr_mcangle_it0.384215133
X-RAY DIFFRACTIONr_scbond_it0.6435725
X-RAY DIFFRACTIONr_scangle_it1.0044.55526
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2826TIGHT POSITIONAL0.040.05
1A2826TIGHT THERMAL0.090.5
2B2826TIGHT POSITIONAL0.060.05
2B2826TIGHT THERMAL0.120.5
3C2826TIGHT POSITIONAL0.040.05
3C2826TIGHT THERMAL0.070.5
4A92TIGHT POSITIONAL0.040.05
4A75MEDIUM POSITIONAL0.060.5
4A92TIGHT THERMAL0.10.5
4A75MEDIUM THERMAL0.082
5B92TIGHT POSITIONAL0.10.05
5B75MEDIUM POSITIONAL0.140.5
5B92TIGHT THERMAL0.140.5
5B75MEDIUM THERMAL0.152
6C92TIGHT POSITIONAL0.040.05
6C75MEDIUM POSITIONAL0.070.5
6C92TIGHT THERMAL0.070.5
6C75MEDIUM THERMAL0.12
7A248TIGHT POSITIONAL0.030.05
7A244MEDIUM POSITIONAL0.040.5
7A248TIGHT THERMAL0.050.5
7A244MEDIUM THERMAL0.072
8B248TIGHT POSITIONAL0.060.05
8B244MEDIUM POSITIONAL0.080.5
8B248TIGHT THERMAL0.080.5
8B244MEDIUM THERMAL0.132
9C248TIGHT POSITIONAL0.030.05
9C244MEDIUM POSITIONAL0.040.5
9C248TIGHT THERMAL0.050.5
9C244MEDIUM THERMAL0.092
LS refinement shellResolution: 2.721→2.791 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 233 -
Rwork0.296 4175 -
all-4408 -
obs--97.05 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.065-0.05040.45351.3907-0.75733.12160.1445-0.0532-0.004-0.0034-0.04250.05850.10980.0111-0.1020.030.00530.0240.02650.02150.0936-2.8388-32.526430.7809
21.00740.0004-0.46261.4329-0.84743.10510.13760.0539-0.01120.0038-0.04310.0441-0.1156-0.0041-0.09450.0268-0.0089-0.01010.04240.01710.090224.0104-72.185673.1671
31.4603-0.7382-0.0952.4356-0.61622.43260.18390.363-0.1371-0.6022-0.1245-0.10280.54340.202-0.05940.25410.0780.01660.2157-0.02070.16771.1622-28.224488.5556
41.52570.39960.76393.488-2.42695.17910.0718-0.26680.14091.1046-0.1853-0.158-1.27510.23390.11350.4439-0.0788-0.00660.1534-0.02090.129626.9997-76.253615.3415
55.31112.47670.48632.59360.60210.8621-0.05880.0604-0.3052-0.0960.08470.08330.157-0.4958-0.02590.1759-0.05060.02920.43090.0440.3142-13.8109-8.564155.1959
65.84-2.5334-0.60712.59451.07190.66-0.0979-0.04190.40920.0425-0.03850.187-0.06-0.31130.13650.19420.0593-0.0050.52290.02340.377712.734-96.277249.2748
73.537-1.3909-0.78582.46490.76433.37-0.1469-0.1273-0.01270.00280.1238-0.2298-0.31130.32770.02310.0705-0.0320.00110.1762-0.01090.218514.0971-9.508454.4607
83.06830.90161.20972.47471.06294.7523-0.16180.1414-0.0029-0.05850.1837-0.31880.46590.4063-0.0220.08640.02440.03970.1771-0.01380.217440.9017-95.3549.214
90.14331.3729-0.78617.2055-9.79345.5820.2159-0.2107-0.12541.5717-0.3531-0.0938-0.82450.33620.13720.84120.5421-0.24851.42990.30530.650816.9881-16.614871.6958
1013.5526-1.586615.56270.7085-3.093321.1648-0.94021.36310.8059-0.33480.2724-0.0223-0.33160.39610.66780.9689-0.22920.07140.61990.11160.366643.4534-88.114432.25
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-369 - 2
2X-RAY DIFFRACTION2B-369 - 2
3X-RAY DIFFRACTION3C-369 - 2
4X-RAY DIFFRACTION4D-369 - 2
5X-RAY DIFFRACTION5A3 - 100
6X-RAY DIFFRACTION6B3 - 102
7X-RAY DIFFRACTION7C3 - 102
8X-RAY DIFFRACTION8D3 - 103
9X-RAY DIFFRACTION9E26 - 42
10X-RAY DIFFRACTION10F26 - 42

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