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- PDB-3hd6: Crystal Structure of the Human Rhesus Glycoprotein RhCG -

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Basic information

Entry
Database: PDB / ID: 3hd6
TitleCrystal Structure of the Human Rhesus Glycoprotein RhCG
ComponentsAmmonium transporter Rh type C
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / ammonia / channel / rhesus / glycoprotein / transporter / membrane / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP / Ammonia transport / Cell membrane / Transmembrane / Transport
Function / homology
Function and homology information


amine transport / ammonium transmembrane transport => GO:0072488 / Rhesus glycoproteins mediate ammonium transport. / transepithelial ammonium transport / ammonium transmembrane transport / intracellular monoatomic ion homeostasis / ammonium channel activity / regulation of pH / ankyrin binding / homeostatic process ...amine transport / ammonium transmembrane transport => GO:0072488 / Rhesus glycoproteins mediate ammonium transport. / transepithelial ammonium transport / ammonium transmembrane transport / intracellular monoatomic ion homeostasis / ammonium channel activity / regulation of pH / ankyrin binding / homeostatic process / plasma membrane => GO:0005886 / epithelial cell differentiation / cytoplasmic vesicle / basolateral plasma membrane / apical plasma membrane / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
Blood group Rhesus C/E/D polypeptide / Ammonium transporter fold / Ammonium transporter AmtB like domains / Ammonium transporter AmtB-like domain / Ammonium Transporter Family / Ammonium/urea transporter / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ammonium transporter Rh type C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGruswitz, F. / Chaudhary, S. / Ho, J.D. / Pezeshki, B. / Ho, C.-M. / Stroud, R.M. / Center for Structures of Membrane Proteins (CSMP)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Function of human Rh based on structure of RhCG at 2.1 A.
Authors: Gruswitz, F. / Chaudhary, S. / Ho, J.D. / Schlessinger, A. / Pezeshki, B. / Ho, C.M. / Sali, A. / Westhoff, C.M. / Stroud, R.M.
History
DepositionMay 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 31, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.5Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ammonium transporter Rh type C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4712
Polymers54,1791
Non-polymers2921
Water2,090116
1
A: Ammonium transporter Rh type C
hetero molecules

A: Ammonium transporter Rh type C
hetero molecules

A: Ammonium transporter Rh type C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,4136
Polymers162,5363
Non-polymers8773
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area18610 Å2
ΔGint-150 kcal/mol
Surface area37580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.830, 99.830, 101.076
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-593-

HOH

21A-594-

HOH

31A-598-

HOH

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the threefold symmetry axis

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Components

#1: Protein Ammonium transporter Rh type C / Rhesus blood group family type C glycoprotein / Rh family type C glycoprotein / Rh type C ...Rhesus blood group family type C glycoprotein / Rh family type C glycoprotein / Rh type C glycoprotein / Tumor-related protein DRC2 / Rh glycoprotein kidney


Mass: 54178.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: suspension growth of human endothelial kidney cells
Source: (gene. exp.) Homo sapiens (human) / Gene: C15orf6, CDRC2, PDRC2, RHCG, RHGK / Plasmid details: stable transfection / Plasmid: pACMV-tetO-Rho / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q9UBD6
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris pH 8.5 (at 293K), 40% PEG 200 + 20mM Tris pH 7.4 (at 293K), 100mM NaCl, 40mM BOG, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 8, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.1→86.39 Å / Num. all: 33464 / Num. obs: 33449 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Rmerge(I) obs: 0.077 / Rsym value: 0.089 / Net I/σ(I): 39.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.637 / % possible all: 95.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.4.0067refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B9W

3b9w


Resolution: 2.1→86.39 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.507 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19505 1695 5.1 %RANDOM
Rwork0.16837 ---
obs0.16973 31746 99.68 %-
all-33464 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.109 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20.34 Å20 Å2
2--0.69 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.1→86.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3163 0 20 116 3299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223265
X-RAY DIFFRACTIONr_bond_other_d0.0010.022140
X-RAY DIFFRACTIONr_angle_refined_deg1.0181.9414432
X-RAY DIFFRACTIONr_angle_other_deg0.8735191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1335400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15923.188138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60215511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.6761514
X-RAY DIFFRACTIONr_chiral_restr0.0660.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023608
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02733
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4291.51985
X-RAY DIFFRACTIONr_mcbond_other0.0951.5832
X-RAY DIFFRACTIONr_mcangle_it0.7923185
X-RAY DIFFRACTIONr_scbond_it1.20431280
X-RAY DIFFRACTIONr_scangle_it1.8814.51247
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.097→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 136 -
Rwork0.198 2258 -
obs--95.8 %
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)
10.95850.1586-0.4560.9861-0.57044.8534-0.0598-0.0425-0.3746-0.0573-0.0755-0.36730.49840.63090.13530.16170.10960.00140.2276-0.00040.255423.29938.80439.325
210.266-4.17962.342621.8641-3.427723.25430.0449-1.1515-0.73161.58790.09710.1090.2039-0.0002-0.1420.4624-0.08960.0240.43840.01960.09786.65151.22963.678
30.62450.1699-0.09151.4437-0.54570.78590.02280.0213-0.03590.0216-0.0257-0.13730.07130.15570.00290.12450.0170.00190.1734-0.00950.073213.553.09940.231
44.52415.7775-5.702714.2624-10.308516.16090.1175-0.15870.26940.8062-0.3678-0.40750.14330.38690.25030.27820.0538-0.10340.3786-0.00070.209326.97146.56960.63
52.8575-5.41882.891211.1528-7.67839.0003-0.3363-0.20840.07280.84650.2978-0.2203-0.53640.07330.03850.26950.0019-0.14980.2377-0.00650.145919.40647.16559.011
60.6495-0.05370.3311.4186-0.00961.14390.0086-0.06690.00690.11510.0433-0.3348-0.03650.3008-0.05190.08870.0071-0.01080.2369-0.0290.132326.08858.09842.554
742.30323.085310.046210.35732.238611.875-0.12861.43780.5225-0.65310.4294-0.68530.06931.0234-0.30080.2258-0.0080.17270.29230.00070.178827.47960.41616.701
81.4125-0.2721-0.51821.85140.74712.6248-0.055-0.04730.07480.1275-0.0276-0.10110.04940.08390.08260.1365-0.00780.00640.1134-0.00340.08769.0564.22440.069
91.1829-0.0636-0.48161.2143-0.27930.84490.00540.01030.29730.00690.037-0.237-0.20220.2149-0.04240.1835-0.04120.00610.1342-0.0060.125913.88176.30239.761
101.5285-0.32450.52051.6440.13972.9064-0.00740.06570.2313-0.08560.0221-0.412-0.40590.2171-0.01470.1207-0.06460.01130.1791-0.02480.172725.01671.10839.314
1110.3492-9.9689-3.567337.04721.85587.73070.2309-2.18990.240.96280.59-0.8899-0.21720.8298-0.8211.0324-0.2821-0.30350.8378-0.12290.312229.8678.39666.405
124.8327-5.0563-4.01026.69935.617111.6024-0.1407-0.43810.48530.11210.4057-0.8935-0.75380.7989-0.26490.2172-0.0947-0.14030.3569-0.03640.338332.54470.50454.379
132.1066-0.7966-0.811413.228211.283412.2668-0.1465-0.0501-0.0199-0.19230.259-0.3147-0.19250.7304-0.11240.08080.03220.03970.3337-0.02690.249735.32555.47536.214
140.3126-0.9340.21893.28760.05841.9090.09510.12390.0345-0.3102-0.0183-0.28860.05380.4576-0.07680.17050.03230.10530.3522-0.08480.20424.46249.88523.032
1525.986-6.705510.43392.2712-1.839111.44090.51531.6243-0.431-0.4863-0.52920.34950.3281-0.06610.01390.41580.0118-0.06560.3076-0.0770.26617.3345.13220.218
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 33
2X-RAY DIFFRACTION2A34 - 59
3X-RAY DIFFRACTION3A60 - 107
4X-RAY DIFFRACTION4A108 - 114
5X-RAY DIFFRACTION5A115 - 128
6X-RAY DIFFRACTION6A129 - 201
7X-RAY DIFFRACTION7A202 - 207
8X-RAY DIFFRACTION8A208 - 247
9X-RAY DIFFRACTION9A248 - 329
10X-RAY DIFFRACTION10A330 - 360
11X-RAY DIFFRACTION11A361 - 387
12X-RAY DIFFRACTION12A388 - 404
13X-RAY DIFFRACTION13A405 - 417
14X-RAY DIFFRACTION14A418 - 435
15X-RAY DIFFRACTION15A436 - 443

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