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- PDB-3n93: Crystal structure of human CRFR2 alpha extracellular domain in co... -

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Basic information

Entry
Database: PDB / ID: 3n93
TitleCrystal structure of human CRFR2 alpha extracellular domain in complex with Urocortin 3
Components
  • Maltose binding protein-CRFR2 alpha
  • Urocortin-3
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 / positive regulation of membrane potential / varicosity / Class B/2 (Secretin family receptors) / response to corticosterone / detection of maltose stimulus / maltose binding / maltose transport complex / response to starvation ...corticotropin-releasing hormone receptor binding / corticotropin-releasing hormone receptor 2 binding / positive regulation of membrane potential / varicosity / Class B/2 (Secretin family receptors) / response to corticosterone / detection of maltose stimulus / maltose binding / maltose transport complex / response to starvation / maltose transport / maltodextrin transmembrane transport / cellular response to nutrient levels / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to immobilization stress / carbohydrate transport / response to glucose / axon terminus / digestion / hormone-mediated signaling pathway / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / positive regulation of insulin secretion / outer membrane-bounded periplasmic space / cellular response to hypoxia / 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-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Homo Sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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.pdbx_synonyms / _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

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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
B: Maltose binding protein-CRFR2 alpha
C: Urocortin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,7636
Polymers107,9863
Non-polymers7773
Water2,324129
1
A: Maltose binding protein-CRFR2 alpha
B: Maltose binding protein-CRFR2 alpha
C: Urocortin-3
hetero molecules

A: Maltose binding protein-CRFR2 alpha
B: Maltose binding protein-CRFR2 alpha
C: Urocortin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,52612
Polymers215,9736
Non-polymers1,5536
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area16550 Å2
ΔGint-82 kcal/mol
Surface area79920 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-23 kcal/mol
Surface area42040 Å2
MethodPISA
3
A: Maltose binding protein-CRFR2 alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4892
Polymers53,1471
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Maltose binding protein-CRFR2 alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5813
Polymers53,1471
Non-polymers4342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
C: Urocortin-3


Theoretical massNumber of molelcules
Total (without water)1,6931
Polymers1,6931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.278, 208.513, 212.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSALAALAAA-369 - -63 - 366
21LYSLYSALAALABB-369 - -63 - 366
12ALAALALEULEUAA4 - 24376 - 396
22ALAALALEULEUBB4 - 24376 - 396
13SERSERILEILEAA38 - 101410 - 473
23SERSERILEILEBB38 - 101410 - 473

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Maltose binding protein-CRFR2 alpha


Mass: 53146.746 Da / Num. of mol.: 2 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRFR2 alpha / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9*PLUS
#2: Protein/peptide Urocortin-3 / / Urocortin III / Ucn III / Stresscopin


Mass: 1692.963 Da / Num. of mol.: 1 / Fragment: UNP residues 142-157 / Source method: obtained synthetically / Source: (synth.) Homo Sapiens (human) / References: UniProt: Q969E3
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 9% PEG 4000 0.1M Sodium acetate 16% Glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 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: 2.5→50 Å / Num. obs: 42571 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.125 / Net I/σ(I): 19.64
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.3

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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 3C4M

3c4m


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.897 / Occupancy max: 1 / Occupancy min: 1 / SU B: 20.406 / SU ML: 0.215 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2139 5 %RANDOM
Rwork0.22 ---
obs0.222 42505 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 133.14 Å2 / Biso mean: 38.404 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2---2.69 Å20 Å2
3---2.33 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7372 0 52 129 7553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227611
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.96910353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5855947
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41925.727337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.683151235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1121519
X-RAY DIFFRACTIONr_chiral_restr0.0810.21135
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215789
X-RAY DIFFRACTIONr_mcbond_it0.4551.54738
X-RAY DIFFRACTIONr_mcangle_it0.89627580
X-RAY DIFFRACTIONr_scbond_it1.48332871
X-RAY DIFFRACTIONr_scangle_it2.5094.52773
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
12826LOOSE POSITIONAL0.275
12826LOOSE THERMAL1.8110
2155LOOSE POSITIONAL0.345
2155LOOSE THERMAL3.4410
3507LOOSE POSITIONAL0.515
3507LOOSE THERMAL3.5510
LS refinement shellResolution: 2.489→2.554 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 138 -
Rwork0.317 2671 -
all-2809 -
obs--90 %
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)
10.8173-0.5209-0.06892.8934-1.02931.60120.12060.01660.0225-0.0193-0.0987-0.0257-0.0790.0867-0.02190.0333-0.0177-0.01770.03310.02220.042230.057430.84119.8453
21.35430.33380.56992.3498-0.59252.3850.13410.1369-0.2404-0.4014-0.06860.04730.5088-0.1749-0.06550.1716-0.0194-0.0240.1268-0.00660.135326.281488.926724.0338
35.3608-0.9817-2.75870.90230.92732.86850.03690.2879-0.076-0.07030.0298-0.6210.0610.1846-0.06670.1058-0.02170.04010.20690.02270.635341.16754.981343.8433
41.98171.0951.52484.0980.92411.9983-0.1691-0.06880.15850.10330.04920.2263-0.0347-0.11820.11990.0454-0.00370.03360.1420.00320.180513.98653.309642.7192
58.54271.6753-1.871157.462721.999418.1682-1.13371.03971.262-1.00890.10560.7168-2.19340.24771.0280.7001-0.1642-0.41420.36150.27650.575410.610571.567836.3137
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-369 - 2
2X-RAY DIFFRACTION2B-369 - 2
3X-RAY DIFFRACTION3A3 - 101
4X-RAY DIFFRACTION4B3 - 95
5X-RAY DIFFRACTION5C26 - 42

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