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- PDB-4nhh: Structure of 2G12 IgG Dimer -

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Basic information

Entry
Database: PDB / ID: 4nhh
TitleStructure of 2G12 IgG Dimer
Components
  • 2G12 IgG dimer heavy chain
  • 2G12 IgG dimer light chain
  • Hepatitis B virus receptor binding protein
KeywordsIMMUNE SYSTEM / Ig / antibody
Function / homology
Function and homology information


: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Hepatitis B virus receptor binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.5 Å
AuthorsWu, Y. / West Jr., A.P. / Kim, H.J. / Thornton, M.E. / Ward, A.B. / Bjorkman, P.J.
CitationJournal: Cell Rep / Year: 2013
Title: Structural basis for enhanced HIV-1 neutralization by a dimeric immunoglobulin G form of the glycan-recognizing antibody 2G12.
Authors: Wu, Y. / West, A.P. / Kim, H.J. / Thornton, M.E. / Ward, A.B. / Bjorkman, P.J.
History
DepositionNov 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: 2G12 IgG dimer light chain
H: Hepatitis B virus receptor binding protein
K: 2G12 IgG dimer light chain
M: Hepatitis B virus receptor binding protein
A: 2G12 IgG dimer heavy chain
B: 2G12 IgG dimer heavy chain
G: 2G12 IgG dimer light chain
E: Hepatitis B virus receptor binding protein
F: 2G12 IgG dimer light chain
I: Hepatitis B virus receptor binding protein
C: 2G12 IgG dimer heavy chain
D: 2G12 IgG dimer heavy chain
Q: 2G12 IgG dimer light chain
O: Hepatitis B virus receptor binding protein
P: 2G12 IgG dimer light chain
R: Hepatitis B virus receptor binding protein
J: 2G12 IgG dimer heavy chain
N: 2G12 IgG dimer heavy chain


Theoretical massNumber of molelcules
Total (without water)428,57718
Polymers428,57718
Non-polymers00
Water00
1
L: 2G12 IgG dimer light chain
H: Hepatitis B virus receptor binding protein
K: 2G12 IgG dimer light chain
M: Hepatitis B virus receptor binding protein
A: 2G12 IgG dimer heavy chain
B: 2G12 IgG dimer heavy chain
G: 2G12 IgG dimer light chain
E: Hepatitis B virus receptor binding protein
F: 2G12 IgG dimer light chain
I: Hepatitis B virus receptor binding protein
C: 2G12 IgG dimer heavy chain
D: 2G12 IgG dimer heavy chain


Theoretical massNumber of molelcules
Total (without water)285,71812
Polymers285,71812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Q: 2G12 IgG dimer light chain
O: Hepatitis B virus receptor binding protein
P: 2G12 IgG dimer light chain
R: Hepatitis B virus receptor binding protein
J: 2G12 IgG dimer heavy chain
N: 2G12 IgG dimer heavy chain

Q: 2G12 IgG dimer light chain
O: Hepatitis B virus receptor binding protein
P: 2G12 IgG dimer light chain
R: Hepatitis B virus receptor binding protein
J: 2G12 IgG dimer heavy chain
N: 2G12 IgG dimer heavy chain


Theoretical massNumber of molelcules
Total (without water)285,71812
Polymers285,71812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)374.731, 374.731, 64.455
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain L and (resseq 2:212 )
21chain K and (resseq 2:212 )
31chain G and (resseq 2:212 )
41chain F and (resseq 2:212 )
51chain Q and (resseq 2:212 )
61chain P and (resseq 2:212 )
12chain A and (resseq 238:285 or resseq 287:292 or resseq 301:443 )
22chain B and (resseq 238:285 or resseq 287:292 or resseq 301:443 )
32chain C and (resseq 238:285 or resseq 287:292 or resseq 301:443 )
42chain D and (resseq 238:285 or resseq 287:292 or resseq 301:443 )
52chain J and (resseq 238:285 or resseq 287:292 or resseq 301:443 )
62chain N and (resseq 238:285 or resseq 287:292 or resseq 301:443 )
13chain H and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )
23chain M and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )
33chain E and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )
43chain I and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )
53chain O and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )
63chain R and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain L and (resseq 2:212 )L2 - 212
211chain K and (resseq 2:212 )K2 - 212
311chain G and (resseq 2:212 )G2 - 212
411chain F and (resseq 2:212 )F2 - 212
511chain Q and (resseq 2:212 )Q2 - 212
611chain P and (resseq 2:212 )P2 - 212
112chain A and (resseq 238:285 or resseq 287:292 or resseq 301:443 )A238 - 285
122chain A and (resseq 238:285 or resseq 287:292 or resseq 301:443 )A287 - 292
132chain A and (resseq 238:285 or resseq 287:292 or resseq 301:443 )A301 - 443
212chain B and (resseq 238:285 or resseq 287:292 or resseq 301:443 )B238 - 285
222chain B and (resseq 238:285 or resseq 287:292 or resseq 301:443 )B287 - 292
232chain B and (resseq 238:285 or resseq 287:292 or resseq 301:443 )B301 - 443
312chain C and (resseq 238:285 or resseq 287:292 or resseq 301:443 )C238 - 285
322chain C and (resseq 238:285 or resseq 287:292 or resseq 301:443 )C287 - 292
332chain C and (resseq 238:285 or resseq 287:292 or resseq 301:443 )C301 - 443
412chain D and (resseq 238:285 or resseq 287:292 or resseq 301:443 )D238 - 285
422chain D and (resseq 238:285 or resseq 287:292 or resseq 301:443 )D287 - 292
432chain D and (resseq 238:285 or resseq 287:292 or resseq 301:443 )D301 - 443
512chain J and (resseq 238:285 or resseq 287:292 or resseq 301:443 )J238 - 285
522chain J and (resseq 238:285 or resseq 287:292 or resseq 301:443 )J287 - 292
532chain J and (resseq 238:285 or resseq 287:292 or resseq 301:443 )J301 - 443
612chain N and (resseq 238:285 or resseq 287:292 or resseq 301:443 )N238 - 285
622chain N and (resseq 238:285 or resseq 287:292 or resseq 301:443 )N287 - 292
632chain N and (resseq 238:285 or resseq 287:292 or resseq 301:443 )N301 - 443
113chain H and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )H1 - 129
123chain H and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )H130 - 154
133chain H and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )H159 - 180
143chain H and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )H169 - 200
153chain H and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )H189 - 222
213chain M and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )M1 - 127
223chain M and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )M136 - 154
233chain M and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )M171 - 180
243chain M and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )M182 - 200
253chain M and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )M205 - 222
313chain E and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )E1 - 129
323chain E and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )E130 - 154
333chain E and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )E159 - 180
343chain E and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )E169 - 200
353chain E and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )E189 - 222
413chain I and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )I1 - 127
423chain I and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )I130 - 154
433chain I and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )I159 - 180
443chain I and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )I169 - 200
453chain I and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )I189 - 222
513chain O and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )O1 - 127
523chain O and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )O136 - 154
533chain O and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )O171 - 180
543chain O and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )O182 - 200
553chain O and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )O205 - 222
613chain R and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )R1 - 127
623chain R and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )R136 - 154
633chain R and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )R171 - 180
643chain R and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )R182 - 200
653chain R and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )R205 - 222

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody
2G12 IgG dimer light chain


Mass: 23233.904 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein
Hepatitis B virus receptor binding protein


Mass: 24248.408 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PYX1
#3: Protein
2G12 IgG dimer heavy chain


Mass: 23947.131 Da / Num. of mol.: 6 / Fragment: unp residues 139-348
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PYX1*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5% Tascimate, 10% PEGMME5000, 100 mM HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 6→65 Å / Num. all: 10665 / Num. obs: 10665

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 6.5→64.905 Å / SU ML: 1.28 / σ(F): 1.99 / Phase error: 47.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3657 511 4.83 %
Rwork0.3813 --
obs0.3805 10576 98.93 %
all-113124 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 6.5→64.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28972 0 0 0 28972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.03729683
X-RAY DIFFRACTIONf_angle_d1.78240278
X-RAY DIFFRACTIONf_dihedral_angle_d15.92410712
X-RAY DIFFRACTIONf_chiral_restr0.14563
X-RAY DIFFRACTIONf_plane_restr0.0155117
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11L1619X-RAY DIFFRACTIONPOSITIONAL0.803
12K1619X-RAY DIFFRACTIONPOSITIONAL0.803
13G1619X-RAY DIFFRACTIONPOSITIONAL0.001
14F1619X-RAY DIFFRACTIONPOSITIONAL0.803
15Q1619X-RAY DIFFRACTIONPOSITIONAL0.001
16P1619X-RAY DIFFRACTIONPOSITIONAL0.803
21A1574X-RAY DIFFRACTIONPOSITIONAL1.25
22B1574X-RAY DIFFRACTIONPOSITIONAL1.25
23C1575X-RAY DIFFRACTIONPOSITIONAL0.001
24D1574X-RAY DIFFRACTIONPOSITIONAL1.25
25J1575X-RAY DIFFRACTIONPOSITIONAL0.001
26N1574X-RAY DIFFRACTIONPOSITIONAL1.25
31H1433X-RAY DIFFRACTIONPOSITIONAL0.797
32M1433X-RAY DIFFRACTIONPOSITIONAL0.797
33E1456X-RAY DIFFRACTIONPOSITIONAL0.001
34I1435X-RAY DIFFRACTIONPOSITIONAL0.796
35O1446X-RAY DIFFRACTIONPOSITIONAL0.001
36R1433X-RAY DIFFRACTIONPOSITIONAL0.797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.5004-7.15380.42911460.41822463X-RAY DIFFRACTION99
7.1538-8.18730.40481180.42862479X-RAY DIFFRACTION99
8.1873-10.30840.3441120.35982524X-RAY DIFFRACTION99
10.3084-64.90850.34331350.36562599X-RAY DIFFRACTION98

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