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- PDB-4nhg: Crystal Structure of 2G12 IgG Dimer -

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Basic information

Entry
Database: PDB / ID: 4nhg
TitleCrystal Structure of 2G12 IgG Dimer
Components
  • 2G12 IgG dimer heavy chain
  • 2G12 IgG dimer light chain
  • Hepatitis B virus receptor binding protein
KeywordsIMMUNE SYSTEM / Ig fold / 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: 8.001 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 5, 2014Group: Structure summary
Revision 1.2Jul 17, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 27, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_residues / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)437,31618
Polymers437,31618
Non-polymers00
Water00
1
A: 2G12 IgG dimer heavy chain
B: 2G12 IgG dimer light chain
C: 2G12 IgG dimer light chain
D: 2G12 IgG dimer heavy chain
X: Hepatitis B virus receptor binding protein
Y: Hepatitis B virus receptor binding protein

A: 2G12 IgG dimer heavy chain
B: 2G12 IgG dimer light chain
C: 2G12 IgG dimer light chain
D: 2G12 IgG dimer heavy chain
X: Hepatitis B virus receptor binding protein
Y: Hepatitis B virus receptor binding protein


Theoretical massNumber of molelcules
Total (without water)291,54412
Polymers291,54412
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
2
E: 2G12 IgG dimer heavy chain
F: 2G12 IgG dimer light chain
G: 2G12 IgG dimer light chain
I: 2G12 IgG dimer heavy chain
J: Hepatitis B virus receptor binding protein
N: Hepatitis B virus receptor binding protein
H: 2G12 IgG dimer heavy chain
K: 2G12 IgG dimer light chain
L: 2G12 IgG dimer light chain
M: 2G12 IgG dimer heavy chain
O: Hepatitis B virus receptor binding protein
P: Hepatitis B virus receptor binding protein


Theoretical massNumber of molelcules
Total (without water)291,54412
Polymers291,54412
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)246.250, 246.250, 657.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain L and (resseq 2:212 )
21chain K and (resseq 2:212 )
31chain C and (resseq 2:212 )
41chain B and (resseq 2:212 )
51chain G and (resseq 2:212 )
61chain F and (resseq 2:212 )
12chain H and (resseq 1:126 or resseq 135:154 or resseq...
22chain M and (resseq 1:126 or resseq 135:154 or resseq...
32chain A and (resseq 1:126 or resseq 135:154 or resseq...
42chain D and (resseq 1:126 or resseq 135:154 or resseq...
52chain E and (resseq 1:126 or resseq 135:154 or resseq...
62chain I and (resseq 1:126 or resseq 135:154 or resseq...
13chain X and (resseq 238:285 or resseq 287:292 or resseq 301:443 )
23chain Y and (resseq 238:285 or resseq 287:292 or resseq 301:443 )
33chain J and (resseq 238:285 or resseq 287:292 or resseq 301:443 )
43chain N and (resseq 238:285 or resseq 287:292 or resseq 301:443 )
53chain O and (resseq 238:285 or resseq 287:292 or resseq 301:443 )
63chain P and (resseq 238:285 or resseq 287:292 or resseq 301:443 )

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALGLYGLYchain L and (resseq 2:212 )LO2 - 2121 - 211
211VALVALGLYGLYchain K and (resseq 2:212 )KN2 - 2121 - 211
311VALVALGLYGLYchain C and (resseq 2:212 )CC2 - 2121 - 211
411VALVALGLYGLYchain B and (resseq 2:212 )BB2 - 2121 - 211
511VALVALGLYGLYchain G and (resseq 2:212 )GG2 - 2121 - 211
611VALVALGLYGLYchain F and (resseq 2:212 )FF2 - 2121 - 211
112GLUGLUTHRTHRchain H and (resseq 1:126 or resseq 135:154 or resseq...HM1 - 1261 - 126
122ALAALAASPASPchain H and (resseq 1:126 or resseq 135:154 or resseq...HM135 - 154135 - 154
132VALVALLEULEUchain H and (resseq 1:126 or resseq 135:154 or resseq...HM162 - 169162 - 169
142SERSERLEULEUchain H and (resseq 1:126 or resseq 135:154 or resseq...HM171 - 180171 - 180
152SERSERGLYGLYchain H and (resseq 1:126 or resseq 135:154 or resseq...HM182 - 200182 - 200
162ILEILEGLUGLUchain H and (resseq 1:126 or resseq 135:154 or resseq...HM205 - 222205 - 222
212GLUGLUTHRTHRchain M and (resseq 1:126 or resseq 135:154 or resseq...MP1 - 1261 - 126
222ALAALAASPASPchain M and (resseq 1:126 or resseq 135:154 or resseq...MP135 - 154135 - 154
232VALVALLEULEUchain M and (resseq 1:126 or resseq 135:154 or resseq...MP162 - 169162 - 169
242SERSERLEULEUchain M and (resseq 1:126 or resseq 135:154 or resseq...MP171 - 180171 - 180
252SERSERGLYGLYchain M and (resseq 1:126 or resseq 135:154 or resseq...MP182 - 200182 - 200
262ILEILEGLUGLUchain M and (resseq 1:126 or resseq 135:154 or resseq...MP205 - 222205 - 222
312GLUGLUTHRTHRchain A and (resseq 1:126 or resseq 135:154 or resseq...AA1 - 1261 - 126
322ALAALAASPASPchain A and (resseq 1:126 or resseq 135:154 or resseq...AA135 - 154135 - 154
332VALVALLEULEUchain A and (resseq 1:126 or resseq 135:154 or resseq...AA162 - 169162 - 169
342SERSERLEULEUchain A and (resseq 1:126 or resseq 135:154 or resseq...AA171 - 180171 - 180
352SERSERGLYGLYchain A and (resseq 1:126 or resseq 135:154 or resseq...AA182 - 200182 - 200
362ILEILEGLUGLUchain A and (resseq 1:126 or resseq 135:154 or resseq...AA205 - 222205 - 222
412GLUGLUTHRTHRchain D and (resseq 1:126 or resseq 135:154 or resseq...DD1 - 1261 - 126
422ALAALAASPASPchain D and (resseq 1:126 or resseq 135:154 or resseq...DD135 - 154135 - 154
432VALVALLEULEUchain D and (resseq 1:126 or resseq 135:154 or resseq...DD162 - 169162 - 169
442SERSERLEULEUchain D and (resseq 1:126 or resseq 135:154 or resseq...DD171 - 180171 - 180
452SERSERGLYGLYchain D and (resseq 1:126 or resseq 135:154 or resseq...DD182 - 200182 - 200
462ILEILEGLUGLUchain D and (resseq 1:126 or resseq 135:154 or resseq...DD205 - 222205 - 222
512GLUGLUTHRTHRchain E and (resseq 1:126 or resseq 135:154 or resseq...EE1 - 1261 - 126
522ALAALAASPASPchain E and (resseq 1:126 or resseq 135:154 or resseq...EE135 - 154135 - 154
532VALVALLEULEUchain E and (resseq 1:126 or resseq 135:154 or resseq...EE162 - 169162 - 169
542SERSERLEULEUchain E and (resseq 1:126 or resseq 135:154 or resseq...EE171 - 180171 - 180
552SERSERGLYGLYchain E and (resseq 1:126 or resseq 135:154 or resseq...EE182 - 200182 - 200
562ILEILEGLUGLUchain E and (resseq 1:126 or resseq 135:154 or resseq...EE205 - 222205 - 222
612GLUGLUTHRTHRchain I and (resseq 1:126 or resseq 135:154 or resseq...IH1 - 1261 - 126
622ALAALAASPASPchain I and (resseq 1:126 or resseq 135:154 or resseq...IH135 - 154135 - 154
632VALVALLEULEUchain I and (resseq 1:126 or resseq 135:154 or resseq...IH162 - 169162 - 169
642SERSERLEULEUchain I and (resseq 1:126 or resseq 135:154 or resseq...IH171 - 180171 - 180
652SERSERGLYGLYchain I and (resseq 1:126 or resseq 135:154 or resseq...IH182 - 200182 - 200
662ILEILEGLUGLUchain I and (resseq 1:126 or resseq 135:154 or resseq...IH205 - 222205 - 222
113PROPROHISHISchain X and (resseq 238:285 or resseq 287:292 or resseq 301:443 )XK238 - 2851 - 48
123ALAALAARGARGchain X and (resseq 238:285 or resseq 287:292 or resseq 301:443 )XK287 - 29250 - 55
133ARGARGLEULEUchain X and (resseq 238:285 or resseq 287:292 or resseq 301:443 )XK301 - 44364 - 206
213PROPROHISHISchain Y and (resseq 238:285 or resseq 287:292 or resseq 301:443 )YL238 - 2851 - 48
223ALAALAARGARGchain Y and (resseq 238:285 or resseq 287:292 or resseq 301:443 )YL287 - 29250 - 55
233ARGARGLEULEUchain Y and (resseq 238:285 or resseq 287:292 or resseq 301:443 )YL301 - 44364 - 206
313PROPROHISHISchain J and (resseq 238:285 or resseq 287:292 or resseq 301:443 )JI238 - 2851 - 48
323ALAALAARGARGchain J and (resseq 238:285 or resseq 287:292 or resseq 301:443 )JI287 - 29250 - 55
333ARGARGLEULEUchain J and (resseq 238:285 or resseq 287:292 or resseq 301:443 )JI301 - 44364 - 206
413PROPROHISHISchain N and (resseq 238:285 or resseq 287:292 or resseq 301:443 )NJ238 - 2851 - 48
423ALAALAARGARGchain N and (resseq 238:285 or resseq 287:292 or resseq 301:443 )NJ287 - 29250 - 55
433ARGARGLEULEUchain N and (resseq 238:285 or resseq 287:292 or resseq 301:443 )NJ301 - 44364 - 206
513PROPROHISHISchain O and (resseq 238:285 or resseq 287:292 or resseq 301:443 )OQ238 - 2851 - 48
523ALAALAARGARGchain O and (resseq 238:285 or resseq 287:292 or resseq 301:443 )OQ287 - 29250 - 55
533ARGARGLEULEUchain O and (resseq 238:285 or resseq 287:292 or resseq 301:443 )OQ301 - 44364 - 206
613PROPROHISHISchain P and (resseq 238:285 or resseq 287:292 or resseq 301:443 )PR238 - 2851 - 48
623ALAALAARGARGchain P and (resseq 238:285 or resseq 287:292 or resseq 301:443 )PR287 - 29250 - 55
633ARGARGLEULEUchain P and (resseq 238:285 or resseq 287:292 or resseq 301:443 )PR301 - 44364 - 206

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody
2G12 IgG dimer heavy chain


Mass: 25704.928 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: 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)
#3: Protein
Hepatitis B virus receptor binding protein


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
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: 6.58 Å3/Da / Density % sol: 81.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.2 M ammonium sulfate, 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
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 7.5→39.8 Å / Num. all: 26016 / Num. obs: 12654

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 8.001→39.746 Å / SU ML: 1.21 / σ(F): 1.66 / Phase error: 36.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3692 1264 9.99 %
Rwork0.3589 --
all0.37 12654 -
obs0.3597 12650 96.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 8.001→39.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29250 0 0 0 29250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01829969
X-RAY DIFFRACTIONf_angle_d1.61740689
X-RAY DIFFRACTIONf_dihedral_angle_d16.2810823
X-RAY DIFFRACTIONf_chiral_restr0.1044614
X-RAY DIFFRACTIONf_plane_restr0.0095171
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11L1618X-RAY DIFFRACTIONPOSITIONAL0.095
12K1618X-RAY DIFFRACTIONPOSITIONAL0.095
13C1618X-RAY DIFFRACTIONPOSITIONAL0.095
14B1618X-RAY DIFFRACTIONPOSITIONAL0.087
15G1618X-RAY DIFFRACTIONPOSITIONAL0.129
16F1618X-RAY DIFFRACTIONPOSITIONAL0.096
21H1499X-RAY DIFFRACTIONPOSITIONAL0.093
22M1499X-RAY DIFFRACTIONPOSITIONAL0.093
23A1499X-RAY DIFFRACTIONPOSITIONAL0.084
24D1499X-RAY DIFFRACTIONPOSITIONAL0.076
25E1499X-RAY DIFFRACTIONPOSITIONAL0.089
26I1499X-RAY DIFFRACTIONPOSITIONAL0.096
31X1574X-RAY DIFFRACTIONPOSITIONAL1.25
32Y1574X-RAY DIFFRACTIONPOSITIONAL1.25
33J1575X-RAY DIFFRACTIONPOSITIONAL0.001
34N1574X-RAY DIFFRACTIONPOSITIONAL1.25
35O1575X-RAY DIFFRACTIONPOSITIONAL0.001
36P1574X-RAY DIFFRACTIONPOSITIONAL1.25
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
8.0005-8.3180.35231030.3572934X-RAY DIFFRACTION74
8.318-8.69280.37461400.35731263X-RAY DIFFRACTION100
8.6928-9.14590.36811420.3541276X-RAY DIFFRACTION100
9.1459-9.71110.35171420.37411276X-RAY DIFFRACTION100
9.7111-10.44820.3391430.3321295X-RAY DIFFRACTION100
10.4482-11.47670.32451440.33821289X-RAY DIFFRACTION100
11.4767-13.08520.3481460.34221317X-RAY DIFFRACTION100
13.0852-16.29480.37641490.34481341X-RAY DIFFRACTION100
16.2948-39.74620.48331550.42641395X-RAY DIFFRACTION98

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